From 3fe37526703ddbe1e452de43437dc7c366ce5c9e Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Mon, 9 Jun 2025 14:45:18 +1000 Subject: [PATCH 01/41] add adir1 class for anopheles dirus data release --- adir1_explore.ipynb | 451 ++++++++++++++++++++++++++++++++++++ malariagen_data/__init__.py | 1 + malariagen_data/adir1.py | 208 +++++++++++++++++ 3 files changed, 660 insertions(+) create mode 100644 adir1_explore.ipynb create mode 100644 malariagen_data/adir1.py diff --git a/adir1_explore.ipynb b/adir1_explore.ipynb new file mode 100644 index 000000000..c42d93dd5 --- /dev/null +++ b/adir1_explore.ipynb @@ -0,0 +1,451 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import malariagen_data" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "'use strict';\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " const force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + "const JS_MIME_TYPE = 'application/javascript';\n", + " const HTML_MIME_TYPE = 'text/html';\n", + " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " const CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " const script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\n", + " const cell = handle.cell;\n", + "\n", + " const id = cell.output_area._bokeh_element_id;\n", + " const server_id = cell.output_area._bokeh_server_id;\n", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(id)\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd_clean, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " const id = msg.content.text.trim()\n", + " drop(id)\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd_destroy);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " const output_area = handle.output_area;\n", + " const output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " const bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " const script_attrs = bk_div.children[0].attributes;\n", + " for (let i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " const toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded(error = null) {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " const html = (() => {\n", + " if (typeof root.Bokeh === \"undefined\") {\n", + " if (error == null) {\n", + " return \"BokehJS is loading ...\";\n", + " } else {\n", + " return \"BokehJS failed to load.\";\n", + " }\n", + " } else {\n", + " const prefix = `BokehJS ${root.Bokeh.version}`;\n", + " if (error == null) {\n", + " return `${prefix} successfully loaded.`;\n", + " } else {\n", + " return `${prefix} encountered errors while loading and may not function as expected.`;\n", + " }\n", + " }\n", + " })();\n", + " el.innerHTML = html;\n", + "\n", + " if (error != null) {\n", + " const wrapper = document.createElement(\"div\");\n", + " wrapper.style.overflow = \"auto\";\n", + " wrapper.style.height = \"5em\";\n", + " wrapper.style.resize = \"vertical\";\n", + " const content = document.createElement(\"div\");\n", + " content.style.fontFamily = \"monospace\";\n", + " content.style.whiteSpace = \"pre-wrap\";\n", + " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", + " content.textContent = error.stack ?? error.toString();\n", + " wrapper.append(content);\n", + " el.append(wrapper);\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(() => display_loaded(error), 100);\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " try {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "\n", + " } catch (error) {throw error;\n", + " }} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Init API\n", + "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "f171c3b7-30c2-4e9f-9133-22206985de07", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'KB672868'" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Are the contigs here? \n", + "chroms = adir1.contigs[:5]\n", + "chroms[1]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "ename": "FileNotFoundError", + "evalue": "b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:426\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 425\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_sets\u001b[49m\u001b[43m[\u001b[49m\u001b[43mrelease\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n", + "\u001b[0;31mKeyError\u001b[0m: '1.x'", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m snps \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msnp_calls\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868:1000000-2000000\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/snp_data.py:1007\u001b[0m, in \u001b[0;36mAnophelesSnpData.snp_calls\u001b[0;34m(self, region, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, inline_array, chunks, cohort_size, min_cohort_size, max_cohort_size, random_seed)\u001b[0m\n\u001b[1;32m 1001\u001b[0m base_params\u001b[38;5;241m.\u001b[39mvalidate_sample_selection_params(\n\u001b[1;32m 1002\u001b[0m sample_query\u001b[38;5;241m=\u001b[39msample_query, sample_indices\u001b[38;5;241m=\u001b[39msample_indices\n\u001b[1;32m 1003\u001b[0m )\n\u001b[1;32m 1005\u001b[0m \u001b[38;5;66;03m# Normalise parameters.\u001b[39;00m\n\u001b[1;32m 1006\u001b[0m sample_sets_prepped: Tuple[\u001b[38;5;28mstr\u001b[39m, \u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mtuple\u001b[39m(\n\u001b[0;32m-> 1007\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_sets_param\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1008\u001b[0m )\n\u001b[1;32m 1009\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m sample_sets\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_indices \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:524\u001b[0m, in \u001b[0;36mAnophelesBase._prep_sample_sets_param\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_prep_sample_sets_param\u001b[39m(\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets]\n\u001b[1;32m 519\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m List[\u001b[38;5;28mstr\u001b[39m]:\n\u001b[1;32m 520\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Common handling for the `sample_sets` parameter. For convenience, we\u001b[39;00m\n\u001b[1;32m 521\u001b[0m \u001b[38;5;124;03m allow this to be a single sample set, or a list of sample sets, or a\u001b[39;00m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;124;03m release identifier, or a list of release identifiers.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 524\u001b[0m all_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_list()\n\u001b[1;32m 526\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_sets \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 527\u001b[0m \u001b[38;5;66;03m# All available sample sets.\u001b[39;00m\n\u001b[1;32m 528\u001b[0m prepped_sample_sets \u001b[38;5;241m=\u001b[39m all_sample_sets\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets(release\u001b[38;5;241m=\u001b[39mr) \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrelease\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mr\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:430\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release]\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n\u001b[0;32m--> 430\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_sample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43msingle_release\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrelease\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 431\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release] \u001b[38;5;241m=\u001b[39m df\n\u001b[1;32m 433\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(release, Sequence):\n\u001b[1;32m 434\u001b[0m \u001b[38;5;66;03m# Ensure no duplicates.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:376\u001b[0m, in \u001b[0;36mAnophelesBase._read_sample_sets\u001b[0;34m(self, single_release)\u001b[0m\n\u001b[1;32m 373\u001b[0m manifest_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrelease_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/manifest.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 375\u001b[0m \u001b[38;5;66;03m# Read the manifest into a pandas dataframe.\u001b[39;00m\n\u001b[0;32m--> 376\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmanifest_path\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 377\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mread_csv(f, sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, na_values\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 379\u001b[0m \u001b[38;5;66;03m# Add a \"release\" column for convenience.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:218\u001b[0m, in \u001b[0;36mAnophelesBase.open_file\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_file\u001b[39m(\u001b[38;5;28mself\u001b[39m, path: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m IO:\n\u001b[1;32m 217\u001b[0m full_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_base_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 218\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfull_path\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1154\u001b[0m, in \u001b[0;36mAbstractFileSystem.open\u001b[0;34m(self, path, mode, block_size, cache_options, compression, **kwargs)\u001b[0m\n\u001b[1;32m 1152\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1153\u001b[0m ac \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mautocommit\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_intrans)\n\u001b[0;32m-> 1154\u001b[0m f \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_open\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1155\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1156\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1157\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1158\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mac\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1159\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1161\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfsspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcompression\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m compr\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1309\u001b[0m, in \u001b[0;36mGCSFileSystem._open\u001b[0;34m(self, path, mode, block_size, cache_options, acl, consistency, metadata, autocommit, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1307\u001b[0m block_size \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_block_size\n\u001b[1;32m 1308\u001b[0m const \u001b[38;5;241m=\u001b[39m consistency \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconsistency\n\u001b[0;32m-> 1309\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mGCSFile\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1311\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1312\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1313\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1314\u001b[0m \u001b[43m 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\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1321\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1468\u001b[0m, in \u001b[0;36mGCSFile.__init__\u001b[0;34m(self, gcsfs, path, mode, block_size, autocommit, cache_type, cache_options, acl, consistency, metadata, content_type, timeout, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1466\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAttempt to open a bucket\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1467\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgeneration \u001b[38;5;241m=\u001b[39m _coalesce_generation(generation, path_generation)\n\u001b[0;32m-> 1468\u001b[0m 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1509\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1510\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdetails\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msize\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m 1511\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcache \u001b[38;5;241m=\u001b[39m caches[cache_type](\n\u001b[1;32m 1512\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mblocksize, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fetch_range, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mcache_options\n\u001b[1;32m 1513\u001b[0m )\n\u001b[1;32m 1514\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1504\u001b[0m, in 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\u001b[49m\u001b[43mgeneration\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneration\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1505\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:115\u001b[0m, in \u001b[0;36msync_wrapper..wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 114\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m obj \u001b[38;5;129;01mor\u001b[39;00m args[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 115\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloop\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:100\u001b[0m, in \u001b[0;36msync\u001b[0;34m(loop, func, timeout, *args, **kwargs)\u001b[0m\n\u001b[1;32m 98\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m FSTimeoutError \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mreturn_result\u001b[39;00m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(return_result, \u001b[38;5;167;01mBaseException\u001b[39;00m):\n\u001b[0;32m--> 100\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m return_result\n\u001b[1;32m 101\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 102\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m return_result\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:55\u001b[0m, in \u001b[0;36m_runner\u001b[0;34m(event, coro, result, timeout)\u001b[0m\n\u001b[1;32m 53\u001b[0m coro \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mwait_for(coro, timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m 54\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 55\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 56\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m ex:\n\u001b[1;32m 57\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m ex\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:797\u001b[0m, in \u001b[0;36mGCSFileSystem._info\u001b[0;34m(self, path, generation, **kwargs)\u001b[0m\n\u001b[1;32m 795\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 796\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdetail\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m \u001b[38;5;66;03m# Force to true for info\u001b[39;00m\n\u001b[0;32m--> 797\u001b[0m out \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ls(path, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 798\u001b[0m out0 \u001b[38;5;241m=\u001b[39m [o \u001b[38;5;28;01mfor\u001b[39;00m o \u001b[38;5;129;01min\u001b[39;00m out \u001b[38;5;28;01mif\u001b[39;00m o[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mrstrip(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m==\u001b[39m path]\n\u001b[1;32m 799\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m out0:\n\u001b[1;32m 800\u001b[0m \u001b[38;5;66;03m# exact hit\u001b[39;00m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:834\u001b[0m, in \u001b[0;36mGCSFileSystem._ls\u001b[0;34m(self, path, detail, prefix, versions, **kwargs)\u001b[0m\n\u001b[1;32m 832\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 833\u001b[0m out \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 834\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m entry \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_list_objects(\n\u001b[1;32m 835\u001b[0m path, prefix\u001b[38;5;241m=\u001b[39mprefix, versions\u001b[38;5;241m=\u001b[39mversions\n\u001b[1;32m 836\u001b[0m ):\n\u001b[1;32m 837\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m versions \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeneration\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m entry:\n\u001b[1;32m 838\u001b[0m entry \u001b[38;5;241m=\u001b[39m entry\u001b[38;5;241m.\u001b[39mcopy()\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:549\u001b[0m, in \u001b[0;36mGCSFileSystem._list_objects\u001b[0;34m(self, path, prefix, versions)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (items \u001b[38;5;241m+\u001b[39m pseudodirs):\n\u001b[1;32m 548\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m key:\n\u001b[0;32m--> 549\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_object(path)]\n\u001b[1;32m 550\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 551\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m []\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:491\u001b[0m, in \u001b[0;36mGCSFileSystem._get_object\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 488\u001b[0m \u001b[38;5;66;03m# Work around various permission settings. Prefer an object get (storage.objects.get), but\u001b[39;00m\n\u001b[1;32m 489\u001b[0m \u001b[38;5;66;03m# fall back to a bucket list + filter to object name (storage.objects.list).\u001b[39;00m\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 491\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_call(\n\u001b[1;32m 492\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGET\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/o/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, bucket, key, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, generation\u001b[38;5;241m=\u001b[39mgeneration\n\u001b[1;32m 493\u001b[0m )\n\u001b[1;32m 494\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 495\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(e)\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mForbidden\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:418\u001b[0m, in \u001b[0;36mGCSFileSystem._call\u001b[0;34m(self, method, path, json_out, info_out, *args, **kwargs)\u001b[0m\n\u001b[1;32m 414\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_call\u001b[39m(\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28mself\u001b[39m, method, path, \u001b[38;5;241m*\u001b[39margs, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, info_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 416\u001b[0m ):\n\u001b[1;32m 417\u001b[0m logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmethod\u001b[38;5;241m.\u001b[39mupper()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00margs\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mheaders\u001b[39m\u001b[38;5;124m'\u001b[39m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 418\u001b[0m status, headers, info, contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_request(\n\u001b[1;32m 419\u001b[0m method, path, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 420\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m json_out:\n\u001b[1;32m 422\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mloads(contents)\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/decorator.py:221\u001b[0m, in \u001b[0;36mdecorate..fun\u001b[0;34m(*args, **kw)\u001b[0m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m kwsyntax:\n\u001b[1;32m 220\u001b[0m args, kw \u001b[38;5;241m=\u001b[39m fix(args, kw, sig)\n\u001b[0;32m--> 221\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m caller(func, \u001b[38;5;241m*\u001b[39m(extras \u001b[38;5;241m+\u001b[39m args), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw)\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:114\u001b[0m, in \u001b[0;36mretry_request\u001b[0;34m(func, retries, *args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39msleep(\u001b[38;5;28mmin\u001b[39m(random\u001b[38;5;241m.\u001b[39mrandom() \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m (retry \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m), \u001b[38;5;241m32\u001b[39m))\n\u001b[0;32m--> 114\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 115\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\n\u001b[1;32m 116\u001b[0m HttpError,\n\u001b[1;32m 117\u001b[0m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 120\u001b[0m aiohttp\u001b[38;5;241m.\u001b[39mclient_exceptions\u001b[38;5;241m.\u001b[39mClientError,\n\u001b[1;32m 121\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 122\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 123\u001b[0m \u001b[38;5;28misinstance\u001b[39m(e, HttpError)\n\u001b[1;32m 124\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m e\u001b[38;5;241m.\u001b[39mcode \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m400\u001b[39m\n\u001b[1;32m 125\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrequester pays\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m e\u001b[38;5;241m.\u001b[39mmessage\n\u001b[1;32m 126\u001b[0m ):\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:411\u001b[0m, in \u001b[0;36mGCSFileSystem._request\u001b[0;34m(self, method, path, headers, json, data, *args, **kwargs)\u001b[0m\n\u001b[1;32m 408\u001b[0m info \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mrequest_info \u001b[38;5;66;03m# for debug only\u001b[39;00m\n\u001b[1;32m 409\u001b[0m contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m r\u001b[38;5;241m.\u001b[39mread()\n\u001b[0;32m--> 411\u001b[0m \u001b[43mvalidate_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstatus\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontents\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 412\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m status, headers, info, contents\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:83\u001b[0m, in \u001b[0;36mvalidate_response\u001b[0;34m(status, content, path, args)\u001b[0m\n\u001b[1;32m 81\u001b[0m path \u001b[38;5;241m=\u001b[39m path\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;241m*\u001b[39m[quote(p) \u001b[38;5;28;01mfor\u001b[39;00m p \u001b[38;5;129;01min\u001b[39;00m args])\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m404\u001b[39m:\n\u001b[0;32m---> 83\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(path)\n\u001b[1;32m 85\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(content, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdecode\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", + "\u001b[0;31mFileNotFoundError\u001b[0m: b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv" + ] + } + ], + "source": [ + "snps = adir1.snp_calls(region=\"KB672868:1000000-2000000\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/malariagen_data/__init__.py b/malariagen_data/__init__.py index dfa555aa7..6bc938825 100644 --- a/malariagen_data/__init__.py +++ b/malariagen_data/__init__.py @@ -1,5 +1,6 @@ # flake8: noqa from .af1 import Af1 +from .adir1 import Adir1 from .ag3 import Ag3 from .amin1 import Amin1 from .anopheles import AnophelesDataResource, Region diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py new file mode 100644 index 000000000..9b053ca62 --- /dev/null +++ b/malariagen_data/adir1.py @@ -0,0 +1,208 @@ +import sys + +import plotly.express as px # type: ignore + +import malariagen_data +from .anopheles import AnophelesDataResource + +MAJOR_VERSION_NUMBER = 1 +MAJOR_VERSION_PATH = "v1.x" +CONFIG_PATH = "v1.x-config.json" +GCS_DEFAULT_URL = "gs://vo_adir_production_us_central1/" +GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_production_us_central1/v1.x/staging" +GCS_REGION_URLS = { + "us-central1": "gs://vo_adir_production_us_central1", +} +# XPEHH_GWSS_CACHE_NAME = "adir1_xpehh_gwss_v1" +# IHS_GWSS_CACHE_NAME = "adir1_ihs_gwss_v1" + +TAXON_PALETTE = px.colors.qualitative.Plotly +TAXON_COLORS = { + "dirus": TAXON_PALETTE[0], +} + + +class Adir1(AnophelesDataResource): + """Provides access to data from Adir1.x releases. + + Parameters + ---------- + url : str, optional + Base path to data. Defaults to use Google Cloud Storage, or can + be a local path on your file system if data have been downloaded. + site_filters_analysis : str, optional + Site filters analysis version. + bokeh_output_notebook : bool, optional + If True (default), configure bokeh to output plots to the notebook. + results_cache : str, optional + Path to directory on local file system to save results. + log : str or stream, optional + File path or stream output for logging messages. + debug : bool, optional + Set to True to enable debug level logging. + show_progress : bool, optional + If True, show a progress bar during longer-running computations. The default can be overridden using an environmental variable named MGEN_SHOW_PROGRESS. + check_location : bool, optional + If True, use ipinfo to check the location of the client system. + **kwargs + Passed through to fsspec when setting up file system access. + + Examples + -------- + Access data from Google Cloud Storage (default): + + >>> import malariagen_data + >>> adir1 = malariagen_data.Adir1() + + Access data downloaded to a local file system: + + >>> adir1 = malariagen_data.Adir1("/local/path/to/vo_adir_release/") + + Access data from Google Cloud Storage, with caching on the local file system + in a directory named "gcs_cache": + + >>> adir1 = malariagen_data.Adir1( + ... "simplecache::gs://vo_adir_production_us_central1", + ... simplecache=dict(cache_storage="gcs_cache"), + ... ) + + Set up caching of some longer-running computations on the local file system, + in a directory named "results_cache": + + >>> adir1 = malariagen_data.Adir1(results_cache="results_cache") + + """ + + # _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME + # _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME + + def __init__( + self, + url=None, + bokeh_output_notebook=True, + results_cache=None, + log=sys.stdout, + debug=False, + show_progress=None, + check_location=True, + cohorts_analysis=None, + site_filters_analysis=None, + discordant_read_calls_analysis=None, + pre=False, + tqdm_class=None, + **storage_options, # used by fsspec via init_filesystem() + ): + super().__init__( + url=url, + config_path=CONFIG_PATH, + cohorts_analysis=cohorts_analysis, + aim_analysis=None, + aim_metadata_dtype=None, + aim_ids=None, + aim_palettes=None, + site_filters_analysis=site_filters_analysis, + discordant_read_calls_analysis=discordant_read_calls_analysis, + default_site_mask="funestus", + default_phasing_analysis="funestus", + default_coverage_calls_analysis="funestus", + bokeh_output_notebook=bokeh_output_notebook, + results_cache=results_cache, + log=log, + debug=debug, + show_progress=show_progress, + check_location=check_location, + pre=pre, + gcs_default_url=GCS_DEFAULT_URL, + gcs_region_urls=GCS_REGION_URLS, + major_version_number=MAJOR_VERSION_NUMBER, + major_version_path=MAJOR_VERSION_PATH, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + storage_options=storage_options, # used by fsspec via init_filesystem() + tqdm_class=tqdm_class, + taxon_colors=TAXON_COLORS, + virtual_contigs=None, + gene_names=None, + inversion_tag_path=None, + ) + + def __repr__(self): + text = ( + f"\n" + f"Storage URL : {self._url}\n" + f"Data releases available : {', '.join(self.releases)}\n" + f"Results cache : {self._results_cache}\n" + # f"Cohorts analysis : {self._cohorts_analysis}\n" + f"Site filters analysis : {self._site_filters_analysis}\n" + f"Software version : malariagen_data {malariagen_data.__version__}\n" + f"Client location : {self.client_location}\n" + f"---\n" + f"Please note that data are subject to terms of use,\n" + f"for more information see https://www.malariagen.net/data\n" + f"or contact support@malariagen.net. For API documentation see \n" + f"https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/Adir1.html" + ) + return text + + def _repr_html_(self): + html = f""" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
MalariaGEN Adir1 API client
+ Please note that data are subject to terms of use, + for more information see + the MalariaGEN website or contact support@malariagen.net. + See also the Adir1 API docs. +
+ Storage URL + {self._url}
+ Data releases available + {', '.join(self.releases)}
+ Results cache + {self._results_cache}
+ Cohorts analysis + {self._cohorts_analysis}
+ Site filters analysis + {self._site_filters_analysis}
+ Software version + malariagen_data {malariagen_data.__version__}
+ Client location + {self.client_location}
+ """ + return html From 921b9c4c942fb1d10fcbe7350103000ce83c5fc7 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 10 Jun 2025 15:03:15 +1000 Subject: [PATCH 02/41] add notebook exploring / troubleshooting adir1 --- notebooks/adir1_explore.ipynb | 483 ++++++++++++++++++++++++++++++++++ 1 file changed, 483 insertions(+) create mode 100644 notebooks/adir1_explore.ipynb diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb new file mode 100644 index 000000000..1fa71882d --- /dev/null +++ b/notebooks/adir1_explore.ipynb @@ -0,0 +1,483 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import malariagen_data" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "'use strict';\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " const force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + "const JS_MIME_TYPE = 'application/javascript';\n", + " const HTML_MIME_TYPE = 'text/html';\n", + " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " const CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " const script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\n", + " const cell = handle.cell;\n", + "\n", + " const id = cell.output_area._bokeh_element_id;\n", + " const server_id = cell.output_area._bokeh_server_id;\n", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(id)\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd_clean, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " const id = msg.content.text.trim()\n", + " drop(id)\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd_destroy);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " const output_area = handle.output_area;\n", + " const output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " const bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " const script_attrs = bk_div.children[0].attributes;\n", + " for (let i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " const toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"
    \\n\"+\n", + " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", + " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", + " \"
\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded(error = null) {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " const html = (() => {\n", + " if (typeof root.Bokeh === \"undefined\") {\n", + " if (error == null) {\n", + " return \"BokehJS is loading ...\";\n", + " } else {\n", + " return \"BokehJS failed to load.\";\n", + " }\n", + " } else {\n", + " const prefix = `BokehJS ${root.Bokeh.version}`;\n", + " if (error == null) {\n", + " return `${prefix} successfully loaded.`;\n", + " } else {\n", + " return `${prefix} encountered errors while loading and may not function as expected.`;\n", + " }\n", + " }\n", + " })();\n", + " el.innerHTML = html;\n", + "\n", + " if (error != null) {\n", + " const wrapper = document.createElement(\"div\");\n", + " wrapper.style.overflow = \"auto\";\n", + " wrapper.style.height = \"5em\";\n", + " wrapper.style.resize = \"vertical\";\n", + " const content = document.createElement(\"div\");\n", + " content.style.fontFamily = \"monospace\";\n", + " content.style.whiteSpace = \"pre-wrap\";\n", + " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", + " content.textContent = error.stack ?? error.toString();\n", + " wrapper.append(content);\n", + " el.append(wrapper);\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(() => display_loaded(error), 100);\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " try {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "\n", + " } catch (error) {throw error;\n", + " }} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
MalariaGEN Adir1 API client
\n", + " Please note that data are subject to terms of use,\n", + " for more information see \n", + " the MalariaGEN website or contact support@malariagen.net.\n", + " See also the Adir1 API docs.\n", + "
\n", + " Storage URL\n", + " gs://vo_adir_production_us_central1/
\n", + " Data releases available\n", + " 1.x
\n", + " Results cache\n", + " /Users/dennistpw/Projects/malariagen_results
\n", + " Cohorts analysis\n", + " noneyet
\n", + " Site filters analysis\n", + " sc_20250610
\n", + " Software version\n", + " malariagen_data 13.3.0.post33+90e72d5a
\n", + " Client location\n", + " Queensland, Australia
\n", + " " + ], + "text/plain": [ + "\n", + "Storage URL : gs://vo_adir_production_us_central1/\n", + "Data releases available : 1.x\n", + "Results cache : /Users/dennistpw/Projects/malariagen_results\n", + "Site filters analysis : sc_20250610\n", + "Software version : malariagen_data 13.3.0.post33+90e72d5a\n", + "Client location : Queensland, Australia\n", + "---\n", + "Please note that data are subject to terms of use,\n", + "for more information see https://www.malariagen.net/data\n", + "or contact support@malariagen.net. For API documentation see \n", + "https://malariagen.github.io/malariagen-data-python/v13.3.0.post33+90e72d5a/Adir1.html" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Init Adir1 API\n", + "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')\n", + "adir1" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + } + ], + "source": [ + "snps = adir1.snp_calls(region=\"KB672868:1000000-1010000\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", + "metadata": {}, + "outputs": [], + "source": [ + "adir1.pca(region = \"KB672868\", n_snps = 100_000, " + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From e3e45fe81d7a2856fa8f45533161d07ef1966804 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 10 Jun 2025 15:21:09 +1000 Subject: [PATCH 03/41] comment out TOU lookups for metadata --- adir1_explore.ipynb | 451 ----------------------- malariagen_data/anoph/sample_metadata.py | 13 +- notebooks/adir1_explore.ipynb | 47 ++- 3 files changed, 50 insertions(+), 461 deletions(-) delete mode 100644 adir1_explore.ipynb diff --git a/adir1_explore.ipynb b/adir1_explore.ipynb deleted file mode 100644 index c42d93dd5..000000000 --- a/adir1_explore.ipynb +++ /dev/null @@ -1,451 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import malariagen_data" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "application/javascript": [ - "'use strict';\n", - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " const force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - "const JS_MIME_TYPE = 'application/javascript';\n", - " const HTML_MIME_TYPE = 'text/html';\n", - " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " const CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " const script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " function drop(id) {\n", - " const view = Bokeh.index.get_by_id(id)\n", - " if (view != null) {\n", - " view.model.document.clear()\n", - " Bokeh.index.delete(view)\n", - " }\n", - " }\n", - "\n", - " const cell = handle.cell;\n", - "\n", - " const id = cell.output_area._bokeh_element_id;\n", - " const server_id = cell.output_area._bokeh_server_id;\n", - "\n", - " // Clean up Bokeh references\n", - " if (id != null) {\n", - " drop(id)\n", - " }\n", - "\n", - " if (server_id !== undefined) {\n", - " // Clean up Bokeh references\n", - " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", - " cell.notebook.kernel.execute(cmd_clean, {\n", - " iopub: {\n", - " output: function(msg) {\n", - " const id = msg.content.text.trim()\n", - " drop(id)\n", - " }\n", - " }\n", - " });\n", - " // Destroy server and session\n", - " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", - " cell.notebook.kernel.execute(cmd_destroy);\n", - " }\n", - " }\n", - "\n", - " /**\n", - " * Handle when a new output is added\n", - " */\n", - " function handleAddOutput(event, handle) {\n", - " const output_area = handle.output_area;\n", - " const output = handle.output;\n", - "\n", - " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", - " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " const bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " const script_attrs = bk_div.children[0].attributes;\n", - " for (let i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", - " }\n", - " // store reference to server id on output_area\n", - " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", - " }\n", - " }\n", - "\n", - " function register_renderer(events, OutputArea) {\n", - "\n", - " function append_mime(data, metadata, element) {\n", - " // create a DOM node to render to\n", - " const toinsert = this.create_output_subarea(\n", - " metadata,\n", - " CLASS_NAME,\n", - " EXEC_MIME_TYPE\n", - " );\n", - " this.keyboard_manager.register_events(toinsert);\n", - " // Render to node\n", - " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", - " render(props, toinsert[toinsert.length - 1]);\n", - " element.append(toinsert);\n", - " return toinsert\n", - " }\n", - "\n", - " /* Handle when an output is cleared or removed */\n", - " events.on('clear_output.CodeCell', handleClearOutput);\n", - " events.on('delete.Cell', handleClearOutput);\n", - "\n", - " /* Handle when a new output is added */\n", - " events.on('output_added.OutputArea', handleAddOutput);\n", - "\n", - " /**\n", - " * Register the mime type and append_mime function with output_area\n", - " */\n", - " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", - " /* Is output safe? */\n", - " safe: true,\n", - " /* Index of renderer in `output_area.display_order` */\n", - " index: 0\n", - " });\n", - " }\n", - "\n", - " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", - " if (root.Jupyter !== undefined) {\n", - " const events = require('base/js/events');\n", - " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", - "\n", - " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", - " register_renderer(events, OutputArea);\n", - " }\n", - " }\n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", - " root._bokeh_timeout = Date.now() + 5000;\n", - " root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " const NB_LOAD_WARNING = {'data': {'text/html':\n", - " \"
\\n\"+\n", - " \"

\\n\"+\n", - " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", - " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", - " \"

\\n\"+\n", - " \"
    \\n\"+\n", - " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", - " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", - " \"
\\n\"+\n", - " \"\\n\"+\n", - " \"from bokeh.resources import INLINE\\n\"+\n", - " \"output_notebook(resources=INLINE)\\n\"+\n", - " \"\\n\"+\n", - " \"
\"}};\n", - "\n", - " function display_loaded(error = null) {\n", - " const el = document.getElementById(null);\n", - " if (el != null) {\n", - " const html = (() => {\n", - " if (typeof root.Bokeh === \"undefined\") {\n", - " if (error == null) {\n", - " return \"BokehJS is loading ...\";\n", - " } else {\n", - " return \"BokehJS failed to load.\";\n", - " }\n", - " } else {\n", - " const prefix = `BokehJS ${root.Bokeh.version}`;\n", - " if (error == null) {\n", - " return `${prefix} successfully loaded.`;\n", - " } else {\n", - " return `${prefix} encountered errors while loading and may not function as expected.`;\n", - " }\n", - " }\n", - " })();\n", - " el.innerHTML = html;\n", - "\n", - " if (error != null) {\n", - " const wrapper = document.createElement(\"div\");\n", - " wrapper.style.overflow = \"auto\";\n", - " wrapper.style.height = \"5em\";\n", - " wrapper.style.resize = \"vertical\";\n", - " const content = document.createElement(\"div\");\n", - " content.style.fontFamily = \"monospace\";\n", - " content.style.whiteSpace = \"pre-wrap\";\n", - " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", - " content.textContent = error.stack ?? error.toString();\n", - " wrapper.append(content);\n", - " el.append(wrapper);\n", - " }\n", - " } else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(() => display_loaded(error), 100);\n", - " }\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - "\n", - " function on_error(url) {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " for (let i = 0; i < css_urls.length; i++) {\n", - " const url = css_urls[i];\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " for (let i = 0; i < js_urls.length; i++) {\n", - " const url = js_urls[i];\n", - " const element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " };\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", - " const css_urls = [];\n", - "\n", - " const inline_js = [ function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - "function(Bokeh) {\n", - " }\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " if (root.Bokeh !== undefined || force === true) {\n", - " try {\n", - " for (let i = 0; i < inline_js.length; i++) {\n", - " inline_js[i].call(root, root.Bokeh);\n", - " }\n", - "\n", - " } catch (error) {throw error;\n", - " }} else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(run_inline_js, 100);\n", - " } else if (!root._bokeh_failed_load) {\n", - " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", - " root._bokeh_failed_load = true;\n", - " } else if (force !== true) {\n", - " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", - " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", - " }\n", - " }\n", - "\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(css_urls, js_urls, function() {\n", - " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(window));" - ], - "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "# Init API\n", - "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "f171c3b7-30c2-4e9f-9133-22206985de07", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "'KB672868'" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Are the contigs here? \n", - "chroms = adir1.contigs[:5]\n", - "chroms[1]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "ename": "FileNotFoundError", - "evalue": "b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:426\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 425\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_sets\u001b[49m\u001b[43m[\u001b[49m\u001b[43mrelease\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n", - "\u001b[0;31mKeyError\u001b[0m: '1.x'", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m snps \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msnp_calls\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868:1000000-2000000\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/snp_data.py:1007\u001b[0m, in \u001b[0;36mAnophelesSnpData.snp_calls\u001b[0;34m(self, region, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, inline_array, chunks, cohort_size, min_cohort_size, max_cohort_size, random_seed)\u001b[0m\n\u001b[1;32m 1001\u001b[0m base_params\u001b[38;5;241m.\u001b[39mvalidate_sample_selection_params(\n\u001b[1;32m 1002\u001b[0m sample_query\u001b[38;5;241m=\u001b[39msample_query, sample_indices\u001b[38;5;241m=\u001b[39msample_indices\n\u001b[1;32m 1003\u001b[0m )\n\u001b[1;32m 1005\u001b[0m \u001b[38;5;66;03m# Normalise parameters.\u001b[39;00m\n\u001b[1;32m 1006\u001b[0m sample_sets_prepped: Tuple[\u001b[38;5;28mstr\u001b[39m, \u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mtuple\u001b[39m(\n\u001b[0;32m-> 1007\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_sets_param\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1008\u001b[0m )\n\u001b[1;32m 1009\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m sample_sets\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_indices \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:524\u001b[0m, in \u001b[0;36mAnophelesBase._prep_sample_sets_param\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_prep_sample_sets_param\u001b[39m(\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets]\n\u001b[1;32m 519\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m List[\u001b[38;5;28mstr\u001b[39m]:\n\u001b[1;32m 520\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Common handling for the `sample_sets` parameter. For convenience, we\u001b[39;00m\n\u001b[1;32m 521\u001b[0m \u001b[38;5;124;03m allow this to be a single sample set, or a list of sample sets, or a\u001b[39;00m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;124;03m release identifier, or a list of release identifiers.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 524\u001b[0m all_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_list()\n\u001b[1;32m 526\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_sets \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 527\u001b[0m \u001b[38;5;66;03m# All available sample sets.\u001b[39;00m\n\u001b[1;32m 528\u001b[0m prepped_sample_sets \u001b[38;5;241m=\u001b[39m all_sample_sets\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets(release\u001b[38;5;241m=\u001b[39mr) \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrelease\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mr\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:430\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release]\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n\u001b[0;32m--> 430\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_sample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43msingle_release\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrelease\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 431\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release] \u001b[38;5;241m=\u001b[39m df\n\u001b[1;32m 433\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(release, Sequence):\n\u001b[1;32m 434\u001b[0m \u001b[38;5;66;03m# Ensure no duplicates.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:376\u001b[0m, in \u001b[0;36mAnophelesBase._read_sample_sets\u001b[0;34m(self, single_release)\u001b[0m\n\u001b[1;32m 373\u001b[0m manifest_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrelease_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/manifest.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 375\u001b[0m \u001b[38;5;66;03m# Read the manifest into a pandas dataframe.\u001b[39;00m\n\u001b[0;32m--> 376\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmanifest_path\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 377\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mread_csv(f, sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, na_values\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 379\u001b[0m \u001b[38;5;66;03m# Add a \"release\" column for convenience.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:218\u001b[0m, in \u001b[0;36mAnophelesBase.open_file\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_file\u001b[39m(\u001b[38;5;28mself\u001b[39m, path: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m IO:\n\u001b[1;32m 217\u001b[0m full_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_base_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 218\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfull_path\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1154\u001b[0m, in \u001b[0;36mAbstractFileSystem.open\u001b[0;34m(self, path, mode, block_size, cache_options, compression, **kwargs)\u001b[0m\n\u001b[1;32m 1152\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1153\u001b[0m ac \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mautocommit\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_intrans)\n\u001b[0;32m-> 1154\u001b[0m f \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_open\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1155\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1156\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1157\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1158\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mac\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1159\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1161\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfsspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcompression\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m compr\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1309\u001b[0m, in \u001b[0;36mGCSFileSystem._open\u001b[0;34m(self, path, mode, block_size, cache_options, acl, consistency, metadata, autocommit, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1307\u001b[0m block_size \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_block_size\n\u001b[1;32m 1308\u001b[0m const \u001b[38;5;241m=\u001b[39m consistency \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconsistency\n\u001b[0;32m-> 1309\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mGCSFile\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1311\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1312\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1313\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1314\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1315\u001b[0m \u001b[43m \u001b[49m\u001b[43mconsistency\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mconst\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1316\u001b[0m \u001b[43m \u001b[49m\u001b[43mmetadata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmetadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1317\u001b[0m \u001b[43m \u001b[49m\u001b[43macl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43macl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1318\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mautocommit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1319\u001b[0m \u001b[43m \u001b[49m\u001b[43mfixed_key_metadata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfixed_key_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1320\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1321\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1468\u001b[0m, in \u001b[0;36mGCSFile.__init__\u001b[0;34m(self, gcsfs, path, mode, block_size, autocommit, cache_type, cache_options, acl, consistency, metadata, content_type, timeout, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1466\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAttempt to open a bucket\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1467\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgeneration \u001b[38;5;241m=\u001b[39m _coalesce_generation(generation, path_generation)\n\u001b[0;32m-> 1468\u001b[0m \u001b[38;5;28;43msuper\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1469\u001b[0m \u001b[43m \u001b[49m\u001b[43mgcsfs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1470\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1471\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1472\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1473\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mautocommit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1474\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_type\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_type\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1475\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1476\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1477\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1478\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgcsfs \u001b[38;5;241m=\u001b[39m gcsfs\n\u001b[1;32m 1479\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mbucket \u001b[38;5;241m=\u001b[39m bucket\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1510\u001b[0m, in \u001b[0;36mAbstractBufferedFile.__init__\u001b[0;34m(self, fs, path, mode, block_size, autocommit, cache_type, cache_options, size, **kwargs)\u001b[0m\n\u001b[1;32m 1508\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m size\n\u001b[1;32m 1509\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1510\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdetails\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msize\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m 1511\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcache \u001b[38;5;241m=\u001b[39m caches[cache_type](\n\u001b[1;32m 1512\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mblocksize, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fetch_range, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mcache_options\n\u001b[1;32m 1513\u001b[0m )\n\u001b[1;32m 1514\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1504\u001b[0m, in \u001b[0;36mGCSFile.details\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1501\u001b[0m \u001b[38;5;129m@property\u001b[39m\n\u001b[1;32m 1502\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdetails\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[1;32m 1503\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 1504\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minfo\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgeneration\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneration\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1505\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:115\u001b[0m, in \u001b[0;36msync_wrapper..wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 114\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m obj \u001b[38;5;129;01mor\u001b[39;00m args[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 115\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloop\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:100\u001b[0m, in \u001b[0;36msync\u001b[0;34m(loop, func, timeout, *args, **kwargs)\u001b[0m\n\u001b[1;32m 98\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m FSTimeoutError \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mreturn_result\u001b[39;00m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(return_result, \u001b[38;5;167;01mBaseException\u001b[39;00m):\n\u001b[0;32m--> 100\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m return_result\n\u001b[1;32m 101\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 102\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m return_result\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:55\u001b[0m, in \u001b[0;36m_runner\u001b[0;34m(event, coro, result, timeout)\u001b[0m\n\u001b[1;32m 53\u001b[0m coro \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mwait_for(coro, timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m 54\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 55\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 56\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m ex:\n\u001b[1;32m 57\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m ex\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:797\u001b[0m, in \u001b[0;36mGCSFileSystem._info\u001b[0;34m(self, path, generation, **kwargs)\u001b[0m\n\u001b[1;32m 795\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 796\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdetail\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m \u001b[38;5;66;03m# Force to true for info\u001b[39;00m\n\u001b[0;32m--> 797\u001b[0m out \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ls(path, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 798\u001b[0m out0 \u001b[38;5;241m=\u001b[39m [o \u001b[38;5;28;01mfor\u001b[39;00m o \u001b[38;5;129;01min\u001b[39;00m out \u001b[38;5;28;01mif\u001b[39;00m o[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mrstrip(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m==\u001b[39m path]\n\u001b[1;32m 799\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m out0:\n\u001b[1;32m 800\u001b[0m \u001b[38;5;66;03m# exact hit\u001b[39;00m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:834\u001b[0m, in \u001b[0;36mGCSFileSystem._ls\u001b[0;34m(self, path, detail, prefix, versions, **kwargs)\u001b[0m\n\u001b[1;32m 832\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 833\u001b[0m out \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 834\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m entry \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_list_objects(\n\u001b[1;32m 835\u001b[0m path, prefix\u001b[38;5;241m=\u001b[39mprefix, versions\u001b[38;5;241m=\u001b[39mversions\n\u001b[1;32m 836\u001b[0m ):\n\u001b[1;32m 837\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m versions \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeneration\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m entry:\n\u001b[1;32m 838\u001b[0m entry \u001b[38;5;241m=\u001b[39m entry\u001b[38;5;241m.\u001b[39mcopy()\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:549\u001b[0m, in \u001b[0;36mGCSFileSystem._list_objects\u001b[0;34m(self, path, prefix, versions)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (items \u001b[38;5;241m+\u001b[39m pseudodirs):\n\u001b[1;32m 548\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m key:\n\u001b[0;32m--> 549\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_object(path)]\n\u001b[1;32m 550\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 551\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m []\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:491\u001b[0m, in \u001b[0;36mGCSFileSystem._get_object\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 488\u001b[0m \u001b[38;5;66;03m# Work around various permission settings. Prefer an object get (storage.objects.get), but\u001b[39;00m\n\u001b[1;32m 489\u001b[0m \u001b[38;5;66;03m# fall back to a bucket list + filter to object name (storage.objects.list).\u001b[39;00m\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 491\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_call(\n\u001b[1;32m 492\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGET\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/o/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, bucket, key, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, generation\u001b[38;5;241m=\u001b[39mgeneration\n\u001b[1;32m 493\u001b[0m )\n\u001b[1;32m 494\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 495\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(e)\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mForbidden\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:418\u001b[0m, in \u001b[0;36mGCSFileSystem._call\u001b[0;34m(self, method, path, json_out, info_out, *args, **kwargs)\u001b[0m\n\u001b[1;32m 414\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_call\u001b[39m(\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28mself\u001b[39m, method, path, \u001b[38;5;241m*\u001b[39margs, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, info_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 416\u001b[0m ):\n\u001b[1;32m 417\u001b[0m logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmethod\u001b[38;5;241m.\u001b[39mupper()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00margs\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mheaders\u001b[39m\u001b[38;5;124m'\u001b[39m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 418\u001b[0m status, headers, info, contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_request(\n\u001b[1;32m 419\u001b[0m method, path, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 420\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m json_out:\n\u001b[1;32m 422\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mloads(contents)\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/decorator.py:221\u001b[0m, in \u001b[0;36mdecorate..fun\u001b[0;34m(*args, **kw)\u001b[0m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m kwsyntax:\n\u001b[1;32m 220\u001b[0m args, kw \u001b[38;5;241m=\u001b[39m fix(args, kw, sig)\n\u001b[0;32m--> 221\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m caller(func, \u001b[38;5;241m*\u001b[39m(extras \u001b[38;5;241m+\u001b[39m args), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw)\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:114\u001b[0m, in \u001b[0;36mretry_request\u001b[0;34m(func, retries, *args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39msleep(\u001b[38;5;28mmin\u001b[39m(random\u001b[38;5;241m.\u001b[39mrandom() \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m (retry \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m), \u001b[38;5;241m32\u001b[39m))\n\u001b[0;32m--> 114\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 115\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\n\u001b[1;32m 116\u001b[0m HttpError,\n\u001b[1;32m 117\u001b[0m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 120\u001b[0m aiohttp\u001b[38;5;241m.\u001b[39mclient_exceptions\u001b[38;5;241m.\u001b[39mClientError,\n\u001b[1;32m 121\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 122\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 123\u001b[0m \u001b[38;5;28misinstance\u001b[39m(e, HttpError)\n\u001b[1;32m 124\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m e\u001b[38;5;241m.\u001b[39mcode \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m400\u001b[39m\n\u001b[1;32m 125\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrequester pays\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m e\u001b[38;5;241m.\u001b[39mmessage\n\u001b[1;32m 126\u001b[0m ):\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:411\u001b[0m, in \u001b[0;36mGCSFileSystem._request\u001b[0;34m(self, method, path, headers, json, data, *args, **kwargs)\u001b[0m\n\u001b[1;32m 408\u001b[0m info \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mrequest_info \u001b[38;5;66;03m# for debug only\u001b[39;00m\n\u001b[1;32m 409\u001b[0m contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m r\u001b[38;5;241m.\u001b[39mread()\n\u001b[0;32m--> 411\u001b[0m \u001b[43mvalidate_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstatus\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontents\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 412\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m status, headers, info, contents\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:83\u001b[0m, in \u001b[0;36mvalidate_response\u001b[0;34m(status, content, path, args)\u001b[0m\n\u001b[1;32m 81\u001b[0m path \u001b[38;5;241m=\u001b[39m path\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;241m*\u001b[39m[quote(p) \u001b[38;5;28;01mfor\u001b[39;00m p \u001b[38;5;129;01min\u001b[39;00m args])\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m404\u001b[39m:\n\u001b[0;32m---> 83\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(path)\n\u001b[1;32m 85\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(content, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdecode\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", - "\u001b[0;31mFileNotFoundError\u001b[0m: b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv" - ] - } - ], - "source": [ - "snps = adir1.snp_calls(region=\"KB672868:1000000-2000000\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index 3088508ba..ebe052de6 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -156,15 +156,16 @@ def _parse_general_metadata( axis="columns", ) + # Have commented these out for now as a) this is not a public release and b) for some reason it breaks everything and I haven't had the time to work out why # Add study columns. - study_info = self.lookup_study_info(sample_set=sample_set) - for column in study_info: - df[column] = study_info[column] + # study_info = self.lookup_study_info(sample_set=sample_set) + # for column in study_info: + # df[column] = study_info[column] # Add terms-of-use columns. - terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) - for column in terms_of_use_info: - df[column] = terms_of_use_info[column] + # terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) + # for column in terms_of_use_info: + # df[column] = terms_of_use_info[column] return df diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb index 1fa71882d..450596a2f 100644 --- a/notebooks/adir1_explore.ipynb +++ b/notebooks/adir1_explore.ipynb @@ -450,12 +450,51 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + }, + { + "ename": "KeyError", + "evalue": "\"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:581\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 579\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 580\u001b[0m \u001b[38;5;66;03m# Attempt to retrieve from the cache.\u001b[39;00m\n\u001b[0;32m--> 581\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_metadata\u001b[49m\u001b[43m[\u001b[49m\u001b[43mcache_key\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n", + "\u001b[0;31mKeyError\u001b[0m: ('1276-AD-BD-ALAM-VMF00156', '1277-VO-KH-WITKOWSKI-VMF00151', '1277-VO-KH-WITKOWSKI-VMF00183', '1278-VO-TH-KOBYLINSKI-VMF00153')", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m100_000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:89\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 83\u001b[0m name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpca_v4\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;66;03m# Normalize params for consistent hash value.\u001b[39;00m\n\u001b[1;32m 86\u001b[0m (\n\u001b[1;32m 87\u001b[0m sample_sets_prepped,\n\u001b[1;32m 88\u001b[0m sample_indices_prepped,\n\u001b[0;32m---> 89\u001b[0m ) \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_selection_cache_params\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 90\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 91\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 93\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 94\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 95\u001b[0m region_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_region_cache_param(region\u001b[38;5;241m=\u001b[39mregion)\n\u001b[1;32m 96\u001b[0m site_mask_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_optional_site_mask_param(site_mask\u001b[38;5;241m=\u001b[39msite_mask)\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:892\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._prep_sample_selection_cache_params\u001b[0;34m(self, sample_sets, sample_query, sample_query_options, sample_indices)\u001b[0m\n\u001b[1;32m 885\u001b[0m sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_sample_sets_param(sample_sets\u001b[38;5;241m=\u001b[39msample_sets)\n\u001b[1;32m 887\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_query \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 888\u001b[0m \u001b[38;5;66;03m# Resolve query to a list of integers for more cache hits - we\u001b[39;00m\n\u001b[1;32m 889\u001b[0m \u001b[38;5;66;03m# do this because there are different ways to write the same pandas\u001b[39;00m\n\u001b[1;32m 890\u001b[0m \u001b[38;5;66;03m# query, and so it's better to evaluate the query and use a list of\u001b[39;00m\n\u001b[1;32m 891\u001b[0m \u001b[38;5;66;03m# integer indices instead.\u001b[39;00m\n\u001b[0;32m--> 892\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 893\u001b[0m sample_query_options \u001b[38;5;241m=\u001b[39m sample_query_options \u001b[38;5;129;01mor\u001b[39;00m {}\n\u001b[1;32m 894\u001b[0m loc_samples \u001b[38;5;241m=\u001b[39m df_samples\u001b[38;5;241m.\u001b[39meval(sample_query, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msample_query_options)\u001b[38;5;241m.\u001b[39mvalues\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:589\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 584\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_spinner(desc\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLoad sample metadata\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m 585\u001b[0m \u001b[38;5;66;03m## Build a single DataFrame using all available metadata.\u001b[39;00m\n\u001b[1;32m 586\u001b[0m \n\u001b[1;32m 587\u001b[0m \u001b[38;5;66;03m# Get the general sample metadata.\u001b[39;00m\n\u001b[1;32m 588\u001b[0m \u001b[38;5;66;03m# Note: this includes study and terms-of-use info.\u001b[39;00m\n\u001b[0;32m--> 589\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneral_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprepped_sample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[38;5;66;03m# Merge with the sequence QC metadata.\u001b[39;00m\n\u001b[1;32m 592\u001b[0m df_sequence_qc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequence_qc_metadata(\n\u001b[1;32m 593\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39mprepped_sample_sets\n\u001b[1;32m 594\u001b[0m )\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:185\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.general_metadata\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 175\u001b[0m \u001b[38;5;129m@doc\u001b[39m(\n\u001b[1;32m 176\u001b[0m summary\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28mself\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 184\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame:\n\u001b[0;32m--> 185\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_metadata_paths\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 186\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_template\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{release_path}\u001b[39;49;00m\u001b[38;5;124;43m/metadata/general/\u001b[39;49m\u001b[38;5;132;43;01m{sample_set}\u001b[39;49;00m\u001b[38;5;124;43m/samples.meta.csv\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 187\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_metadata_func\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_general_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 188\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:119\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_metadata_paths\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 117\u001b[0m path \u001b[38;5;241m=\u001b[39m file_paths[sample_set]\n\u001b[1;32m 118\u001b[0m data \u001b[38;5;241m=\u001b[39m files[path]\n\u001b[0;32m--> 119\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mparse_metadata_func\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 120\u001b[0m dfs\u001b[38;5;241m.\u001b[39mappend(df)\n\u001b[1;32m 122\u001b[0m \u001b[38;5;66;03m# Concatenate all DataFrames.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:160\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_general_metadata\u001b[0;34m(self, sample_set, data)\u001b[0m\n\u001b[1;32m 154\u001b[0m df[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mquarter\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m df\u001b[38;5;241m.\u001b[39mapply(\n\u001b[1;32m 155\u001b[0m \u001b[38;5;28;01mlambda\u001b[39;00m row: ((row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m3\u001b[39m) \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 156\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 157\u001b[0m )\n\u001b[1;32m 159\u001b[0m \u001b[38;5;66;03m# Add study columns.\u001b[39;00m\n\u001b[0;32m--> 160\u001b[0m study_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlookup_study_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_set\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m column \u001b[38;5;129;01min\u001b[39;00m study_info:\n\u001b[1;32m 162\u001b[0m df[column] \u001b[38;5;241m=\u001b[39m study_info[column]\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:487\u001b[0m, in \u001b[0;36mAnophelesBase.lookup_study_info\u001b[0;34m(self, sample_set)\u001b[0m\n\u001b[1;32m 485\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 486\u001b[0m df_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets()\u001b[38;5;241m.\u001b[39mset_index(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 487\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;241m=\u001b[39m \u001b[43mdf_sample_sets\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_url\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mto_dict(orient\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 491\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info[sample_set]\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/frame.py:3766\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 3764\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_iterator(key):\n\u001b[1;32m 3765\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 3766\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcolumns\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 3768\u001b[0m \u001b[38;5;66;03m# take() does not accept boolean indexers\u001b[39;00m\n\u001b[1;32m 3769\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(indexer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m==\u001b[39m \u001b[38;5;28mbool\u001b[39m:\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5935\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5933\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m use_interval_msg:\n\u001b[1;32m 5934\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[1;32m 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "\u001b[0;31mKeyError\u001b[0m: \"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"" + ] + } + ], "source": [ - "adir1.pca(region = \"KB672868\", n_snps = 100_000, " + "pca = adir1.pca(region = \"KB672868\", n_snps = 100_000, sample_query = \"country == 'Thailand'\")" ] } ], From b8ed3cba756c42365e9f2876847c4b3bb05451fd Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Thu, 12 Jun 2025 08:39:04 +1000 Subject: [PATCH 04/41] add annotation to commented out bit of metadata --- malariagen_data/anoph/sample_metadata.py | 34 +- notebooks/adir1_explore.ipynb | 522 ----------------------- 2 files changed, 18 insertions(+), 538 deletions(-) delete mode 100644 notebooks/adir1_explore.ipynb diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index ebe052de6..fc0d24540 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -589,29 +589,31 @@ def sample_metadata( # Note: this includes study and terms-of-use info. df_samples = self.general_metadata(sample_sets=prepped_sample_sets) + # Commented this out as it breaks some things - will fix + # Merge with the sequence QC metadata. - df_sequence_qc = self.sequence_qc_metadata( - sample_sets=prepped_sample_sets - ) + # df_sequence_qc = self.sequence_qc_metadata( + # sample_sets=prepped_sample_sets + # ) # Note: merging can change column dtypes - df_samples = df_samples.merge( - df_sequence_qc, on="sample_id", sort=False, how="left" - ) + # df_samples = df_samples.merge( + # df_sequence_qc, on="sample_id", sort=False, how="left" + # ) # If available, merge with the AIM metadata. - if self._aim_analysis: - df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) - df_samples = df_samples.merge( - df_aim, on="sample_id", sort=False, how="left" - ) + # if self._aim_analysis: + # df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) + # df_samples = df_samples.merge( + # df_aim, on="sample_id", sort=False, how="left" + # ) # If available, merge with the cohorts metadata. - if self._cohorts_analysis: - df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) - df_samples = df_samples.merge( - df_cohorts, on="sample_id", sort=False, how="left" - ) + # if self._cohorts_analysis: + # df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) + # df_samples = df_samples.merge( + # df_cohorts, on="sample_id", sort=False, how="left" + # ) # Store sample metadata in the cache. self._cache_sample_metadata[cache_key] = df_samples diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb deleted file mode 100644 index 450596a2f..000000000 --- a/notebooks/adir1_explore.ipynb +++ /dev/null @@ -1,522 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import malariagen_data" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "application/javascript": [ - "'use strict';\n", - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " const force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - "const JS_MIME_TYPE = 'application/javascript';\n", - " const HTML_MIME_TYPE = 'text/html';\n", - " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " const CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " const script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " function drop(id) {\n", - " const view = Bokeh.index.get_by_id(id)\n", - " if (view != null) {\n", - " view.model.document.clear()\n", - " Bokeh.index.delete(view)\n", - " }\n", - " }\n", - "\n", - " const cell = handle.cell;\n", - "\n", - " const id = cell.output_area._bokeh_element_id;\n", - " const server_id = cell.output_area._bokeh_server_id;\n", - "\n", - " // Clean up Bokeh references\n", - " if (id != null) {\n", - " drop(id)\n", - " }\n", - "\n", - " if (server_id !== undefined) {\n", - " // Clean up Bokeh references\n", - " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", - " cell.notebook.kernel.execute(cmd_clean, {\n", - " iopub: {\n", - " output: function(msg) {\n", - " const id = msg.content.text.trim()\n", - " drop(id)\n", - " }\n", - " }\n", - " });\n", - " // Destroy server and session\n", - " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", - " cell.notebook.kernel.execute(cmd_destroy);\n", - " }\n", - " }\n", - "\n", - " /**\n", - " * Handle when a new output is added\n", - " */\n", - " function handleAddOutput(event, handle) {\n", - " const output_area = handle.output_area;\n", - " const output = handle.output;\n", - "\n", - " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", - " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " const bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " const script_attrs = bk_div.children[0].attributes;\n", - " for (let i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", - " }\n", - " // store reference to server id on output_area\n", - " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", - " }\n", - " }\n", - "\n", - " function register_renderer(events, OutputArea) {\n", - "\n", - " function append_mime(data, metadata, element) {\n", - " // create a DOM node to render to\n", - " const toinsert = this.create_output_subarea(\n", - " metadata,\n", - " CLASS_NAME,\n", - " EXEC_MIME_TYPE\n", - " );\n", - " this.keyboard_manager.register_events(toinsert);\n", - " // Render to node\n", - " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", - " render(props, toinsert[toinsert.length - 1]);\n", - " element.append(toinsert);\n", - " return toinsert\n", - " }\n", - "\n", - " /* Handle when an output is cleared or removed */\n", - " events.on('clear_output.CodeCell', handleClearOutput);\n", - " events.on('delete.Cell', handleClearOutput);\n", - "\n", - " /* Handle when a new output is added */\n", - " events.on('output_added.OutputArea', handleAddOutput);\n", - "\n", - " /**\n", - " * Register the mime type and append_mime function with output_area\n", - " */\n", - " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", - " /* Is output safe? */\n", - " safe: true,\n", - " /* Index of renderer in `output_area.display_order` */\n", - " index: 0\n", - " });\n", - " }\n", - "\n", - " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", - " if (root.Jupyter !== undefined) {\n", - " const events = require('base/js/events');\n", - " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", - "\n", - " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", - " register_renderer(events, OutputArea);\n", - " }\n", - " }\n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", - " root._bokeh_timeout = Date.now() + 5000;\n", - " root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " const NB_LOAD_WARNING = {'data': {'text/html':\n", - " \"
\\n\"+\n", - " \"

\\n\"+\n", - " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", - " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", - " \"

\\n\"+\n", - " \"
    \\n\"+\n", - " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", - " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", - " \"
\\n\"+\n", - " \"\\n\"+\n", - " \"from bokeh.resources import INLINE\\n\"+\n", - " \"output_notebook(resources=INLINE)\\n\"+\n", - " \"\\n\"+\n", - " \"
\"}};\n", - "\n", - " function display_loaded(error = null) {\n", - " const el = document.getElementById(null);\n", - " if (el != null) {\n", - " const html = (() => {\n", - " if (typeof root.Bokeh === \"undefined\") {\n", - " if (error == null) {\n", - " return \"BokehJS is loading ...\";\n", - " } else {\n", - " return \"BokehJS failed to load.\";\n", - " }\n", - " } else {\n", - " const prefix = `BokehJS ${root.Bokeh.version}`;\n", - " if (error == null) {\n", - " return `${prefix} successfully loaded.`;\n", - " } else {\n", - " return `${prefix} encountered errors while loading and may not function as expected.`;\n", - " }\n", - " }\n", - " })();\n", - " el.innerHTML = html;\n", - "\n", - " if (error != null) {\n", - " const wrapper = document.createElement(\"div\");\n", - " wrapper.style.overflow = \"auto\";\n", - " wrapper.style.height = \"5em\";\n", - " wrapper.style.resize = \"vertical\";\n", - " const content = document.createElement(\"div\");\n", - " content.style.fontFamily = \"monospace\";\n", - " content.style.whiteSpace = \"pre-wrap\";\n", - " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", - " content.textContent = error.stack ?? error.toString();\n", - " wrapper.append(content);\n", - " el.append(wrapper);\n", - " }\n", - " } else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(() => display_loaded(error), 100);\n", - " }\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - "\n", - " function on_error(url) {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " for (let i = 0; i < css_urls.length; i++) {\n", - " const url = css_urls[i];\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " for (let i = 0; i < js_urls.length; i++) {\n", - " const url = js_urls[i];\n", - " const element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " };\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", - " const css_urls = [];\n", - "\n", - " const inline_js = [ function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - "function(Bokeh) {\n", - " }\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " if (root.Bokeh !== undefined || force === true) {\n", - " try {\n", - " for (let i = 0; i < inline_js.length; i++) {\n", - " inline_js[i].call(root, root.Bokeh);\n", - " }\n", - "\n", - " } catch (error) {throw error;\n", - " }} else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(run_inline_js, 100);\n", - " } else if (!root._bokeh_failed_load) {\n", - " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", - " root._bokeh_failed_load = true;\n", - " } else if (force !== true) {\n", - " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", - " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", - " }\n", - " }\n", - "\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(css_urls, js_urls, function() {\n", - " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(window));" - ], - "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
MalariaGEN Adir1 API client
\n", - " Please note that data are subject to terms of use,\n", - " for more information see \n", - " the MalariaGEN website or contact support@malariagen.net.\n", - " See also the Adir1 API docs.\n", - "
\n", - " Storage URL\n", - " gs://vo_adir_production_us_central1/
\n", - " Data releases available\n", - " 1.x
\n", - " Results cache\n", - " /Users/dennistpw/Projects/malariagen_results
\n", - " Cohorts analysis\n", - " noneyet
\n", - " Site filters analysis\n", - " sc_20250610
\n", - " Software version\n", - " malariagen_data 13.3.0.post33+90e72d5a
\n", - " Client location\n", - " Queensland, Australia
\n", - " " - ], - "text/plain": [ - "\n", - "Storage URL : gs://vo_adir_production_us_central1/\n", - "Data releases available : 1.x\n", - "Results cache : /Users/dennistpw/Projects/malariagen_results\n", - "Site filters analysis : sc_20250610\n", - "Software version : malariagen_data 13.3.0.post33+90e72d5a\n", - "Client location : Queensland, Australia\n", - "---\n", - "Please note that data are subject to terms of use,\n", - "for more information see https://www.malariagen.net/data\n", - "or contact support@malariagen.net. For API documentation see \n", - "https://malariagen.github.io/malariagen-data-python/v13.3.0.post33+90e72d5a/Adir1.html" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Init Adir1 API\n", - "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')\n", - "adir1" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " \r" - ] - } - ], - "source": [ - "snps = adir1.snp_calls(region=\"KB672868:1000000-1010000\")" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " \r" - ] - }, - { - "ename": "KeyError", - "evalue": "\"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:581\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 579\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 580\u001b[0m \u001b[38;5;66;03m# Attempt to retrieve from the cache.\u001b[39;00m\n\u001b[0;32m--> 581\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_metadata\u001b[49m\u001b[43m[\u001b[49m\u001b[43mcache_key\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n", - "\u001b[0;31mKeyError\u001b[0m: ('1276-AD-BD-ALAM-VMF00156', '1277-VO-KH-WITKOWSKI-VMF00151', '1277-VO-KH-WITKOWSKI-VMF00183', '1278-VO-TH-KOBYLINSKI-VMF00153')", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m100_000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:89\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 83\u001b[0m name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpca_v4\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;66;03m# Normalize params for consistent hash value.\u001b[39;00m\n\u001b[1;32m 86\u001b[0m (\n\u001b[1;32m 87\u001b[0m sample_sets_prepped,\n\u001b[1;32m 88\u001b[0m sample_indices_prepped,\n\u001b[0;32m---> 89\u001b[0m ) \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_selection_cache_params\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 90\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 91\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 93\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 94\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 95\u001b[0m region_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_region_cache_param(region\u001b[38;5;241m=\u001b[39mregion)\n\u001b[1;32m 96\u001b[0m site_mask_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_optional_site_mask_param(site_mask\u001b[38;5;241m=\u001b[39msite_mask)\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:892\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._prep_sample_selection_cache_params\u001b[0;34m(self, sample_sets, sample_query, sample_query_options, sample_indices)\u001b[0m\n\u001b[1;32m 885\u001b[0m sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_sample_sets_param(sample_sets\u001b[38;5;241m=\u001b[39msample_sets)\n\u001b[1;32m 887\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_query \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 888\u001b[0m \u001b[38;5;66;03m# Resolve query to a list of integers for more cache hits - we\u001b[39;00m\n\u001b[1;32m 889\u001b[0m \u001b[38;5;66;03m# do this because there are different ways to write the same pandas\u001b[39;00m\n\u001b[1;32m 890\u001b[0m \u001b[38;5;66;03m# query, and so it's better to evaluate the query and use a list of\u001b[39;00m\n\u001b[1;32m 891\u001b[0m \u001b[38;5;66;03m# integer indices instead.\u001b[39;00m\n\u001b[0;32m--> 892\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 893\u001b[0m sample_query_options \u001b[38;5;241m=\u001b[39m sample_query_options \u001b[38;5;129;01mor\u001b[39;00m {}\n\u001b[1;32m 894\u001b[0m loc_samples \u001b[38;5;241m=\u001b[39m df_samples\u001b[38;5;241m.\u001b[39meval(sample_query, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msample_query_options)\u001b[38;5;241m.\u001b[39mvalues\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:589\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 584\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_spinner(desc\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLoad sample metadata\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m 585\u001b[0m \u001b[38;5;66;03m## Build a single DataFrame using all available metadata.\u001b[39;00m\n\u001b[1;32m 586\u001b[0m \n\u001b[1;32m 587\u001b[0m \u001b[38;5;66;03m# Get the general sample metadata.\u001b[39;00m\n\u001b[1;32m 588\u001b[0m \u001b[38;5;66;03m# Note: this includes study and terms-of-use info.\u001b[39;00m\n\u001b[0;32m--> 589\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneral_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprepped_sample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[38;5;66;03m# Merge with the sequence QC metadata.\u001b[39;00m\n\u001b[1;32m 592\u001b[0m df_sequence_qc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequence_qc_metadata(\n\u001b[1;32m 593\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39mprepped_sample_sets\n\u001b[1;32m 594\u001b[0m )\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:185\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.general_metadata\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 175\u001b[0m \u001b[38;5;129m@doc\u001b[39m(\n\u001b[1;32m 176\u001b[0m summary\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28mself\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 184\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame:\n\u001b[0;32m--> 185\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_metadata_paths\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 186\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_template\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{release_path}\u001b[39;49;00m\u001b[38;5;124;43m/metadata/general/\u001b[39;49m\u001b[38;5;132;43;01m{sample_set}\u001b[39;49;00m\u001b[38;5;124;43m/samples.meta.csv\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 187\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_metadata_func\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_general_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 188\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:119\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_metadata_paths\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 117\u001b[0m path \u001b[38;5;241m=\u001b[39m file_paths[sample_set]\n\u001b[1;32m 118\u001b[0m data \u001b[38;5;241m=\u001b[39m files[path]\n\u001b[0;32m--> 119\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mparse_metadata_func\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 120\u001b[0m dfs\u001b[38;5;241m.\u001b[39mappend(df)\n\u001b[1;32m 122\u001b[0m \u001b[38;5;66;03m# Concatenate all DataFrames.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:160\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_general_metadata\u001b[0;34m(self, sample_set, data)\u001b[0m\n\u001b[1;32m 154\u001b[0m df[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mquarter\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m df\u001b[38;5;241m.\u001b[39mapply(\n\u001b[1;32m 155\u001b[0m \u001b[38;5;28;01mlambda\u001b[39;00m row: ((row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m3\u001b[39m) \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 156\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 157\u001b[0m )\n\u001b[1;32m 159\u001b[0m \u001b[38;5;66;03m# Add study columns.\u001b[39;00m\n\u001b[0;32m--> 160\u001b[0m study_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlookup_study_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_set\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m column \u001b[38;5;129;01min\u001b[39;00m study_info:\n\u001b[1;32m 162\u001b[0m df[column] \u001b[38;5;241m=\u001b[39m study_info[column]\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:487\u001b[0m, in \u001b[0;36mAnophelesBase.lookup_study_info\u001b[0;34m(self, sample_set)\u001b[0m\n\u001b[1;32m 485\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 486\u001b[0m df_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets()\u001b[38;5;241m.\u001b[39mset_index(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 487\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;241m=\u001b[39m \u001b[43mdf_sample_sets\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_url\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mto_dict(orient\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 491\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info[sample_set]\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/frame.py:3766\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 3764\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_iterator(key):\n\u001b[1;32m 3765\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 3766\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcolumns\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 3768\u001b[0m \u001b[38;5;66;03m# take() does not accept boolean indexers\u001b[39;00m\n\u001b[1;32m 3769\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(indexer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m==\u001b[39m \u001b[38;5;28mbool\u001b[39m:\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5935\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5933\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m use_interval_msg:\n\u001b[1;32m 5934\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[1;32m 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", - "\u001b[0;31mKeyError\u001b[0m: \"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"" - ] - } - ], - "source": [ - "pca = adir1.pca(region = \"KB672868\", n_snps = 100_000, sample_query = \"country == 'Thailand'\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} From 57a9b42a4af550057d3a0986e037b4ed5b9e4ca6 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Sun, 15 Jun 2025 22:28:15 -0500 Subject: [PATCH 05/41] forgot how the alphabet works d'oh --- malariagen_data/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/__init__.py b/malariagen_data/__init__.py index 6bc938825..306896658 100644 --- a/malariagen_data/__init__.py +++ b/malariagen_data/__init__.py @@ -1,6 +1,6 @@ # flake8: noqa -from .af1 import Af1 from .adir1 import Adir1 +from .af1 import Af1 from .ag3 import Ag3 from .amin1 import Amin1 from .anopheles import AnophelesDataResource, Region From ced92247eefea9316d38feb4084d010b01f0f04c Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Mon, 16 Jun 2025 20:35:38 -0500 Subject: [PATCH 06/41] add hashing to roh function --- malariagen_data/adir1.py | 6 +- malariagen_data/anopheles.py | 71 +++++-- poetry.lock | 402 ++++++++++++----------------------- pyproject.toml | 1 + 4 files changed, 193 insertions(+), 287 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index 9b053ca62..c24562426 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -102,9 +102,9 @@ def __init__( aim_palettes=None, site_filters_analysis=site_filters_analysis, discordant_read_calls_analysis=discordant_read_calls_analysis, - default_site_mask="funestus", - default_phasing_analysis="funestus", - default_coverage_calls_analysis="funestus", + default_site_mask="dirus", + default_phasing_analysis="dirus", + default_coverage_calls_analysis="dirus", bokeh_output_notebook=bokeh_output_notebook, results_cache=results_cache, log=log, diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py index 0aec9bd9a..87b42a9e5 100644 --- a/malariagen_data/anopheles.py +++ b/malariagen_data/anopheles.py @@ -572,31 +572,68 @@ def roh_hmm( debug = self._log.debug resolved_region: Region = parse_single_region(self, region) - del region - debug("compute windowed heterozygosity") - sample_id, sample_set, windows, counts = self._sample_count_het( + name = "roh" + + params = dict( sample=sample, - region=resolved_region, - site_mask=site_mask, + region=region, window_size=window_size, + site_mask=site_mask, sample_set=sample_set, - chunks=chunks, - inline_array=inline_array, - ) - - debug("compute runs of homozygosity") - df_roh = self._roh_hmm_predict( - windows=windows, - counts=counts, phet_roh=phet_roh, phet_nonroh=phet_nonroh, transition=transition, - window_size=window_size, - sample_id=sample_id, - contig=resolved_region.contig, + chunks=chunks, + inline_array=inline_array, ) + del region + + try: + # Load cached numeric data, adding str / obj data again. + results = self.results_cache_get(name=name, params=params) + df_roh = pd.DataFrame(results) + df_roh["sample_id"] = sample + df_roh["contig"] = resolved_region.contig + + except CacheMiss: + debug("compute windowed heterozygosity") + sample_id, sample_set, windows, counts = self._sample_count_het( + sample=sample, + region=resolved_region, + site_mask=site_mask, + window_size=window_size, + sample_set=sample_set, + chunks=chunks, + inline_array=inline_array, + ) + + debug("compute runs of homozygosity") + df_roh = self._roh_hmm_predict( + windows=windows, + counts=counts, + phet_roh=phet_roh, + phet_nonroh=phet_nonroh, + transition=transition, + window_size=window_size, + sample_id=sample_id, + contig=resolved_region.contig, + ) + + # Specify numeric columns to save (saving obj - sample ID and contig - breaks the save. + columns_to_save = [ + "roh_start", + "roh_stop", + "roh_length", + "roh_is_marginal", + ] + self.results_cache_set( + name=name, + params=params, + results={col: df_roh[col].to_numpy() for col in columns_to_save}, + ) + return df_roh @check_types @@ -1304,7 +1341,7 @@ def ihs_gwss( ) -> Tuple[np.ndarray, np.ndarray]: # change this name if you ever change the behaviour of this function, to # invalidate any previously cached data - name = self._ihs_gwss_cache_name + name = "roh" params = dict( contig=contig, diff --git a/poetry.lock b/poetry.lock index 619febcb1..d02d5c5bc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. [[package]] name = "accessible-pygments" @@ -7,7 +7,7 @@ description = "A collection of accessible pygments styles" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"}, {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"}, @@ -27,7 +27,6 @@ description = "Async client for aws services using botocore and aiohttp" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aiobotocore-2.15.2-py3-none-any.whl", hash = "sha256:d4d3128b4b558e2b4c369bfa963b022d7e87303adb82eec623cec8aa77ae578a"}, {file = "aiobotocore-2.15.2.tar.gz", hash = "sha256:9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375"}, @@ -50,7 +49,6 @@ description = "Happy Eyeballs for asyncio" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aiohappyeyeballs-2.4.4-py3-none-any.whl", hash = "sha256:a980909d50efcd44795c4afeca523296716d50cd756ddca6af8c65b996e27de8"}, {file = "aiohappyeyeballs-2.4.4.tar.gz", hash = "sha256:5fdd7d87889c63183afc18ce9271f9b0a7d32c2303e394468dd45d514a757745"}, @@ -63,7 +61,6 @@ description = "Async http client/server framework (asyncio)" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aiohttp-3.11.9-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:0411777249f25d11bd2964a230b3ffafcbed6cd65d0f2b132bc2b8f5b8c347c7"}, {file = "aiohttp-3.11.9-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:499368eb904566fbdf1a3836a1532000ef1308f34a1bcbf36e6351904cced771"}, @@ -154,7 +151,7 @@ propcache = ">=0.2.0" yarl = ">=1.17.0,<2.0" [package.extras] -speedups = ["Brotli", "aiodns (>=3.2.0)", "brotlicffi"] +speedups = ["Brotli ; platform_python_implementation == \"CPython\"", "aiodns (>=3.2.0) ; sys_platform == \"linux\" or sys_platform == \"darwin\"", "brotlicffi ; platform_python_implementation != \"CPython\""] [[package]] name = "aioitertools" @@ -163,7 +160,6 @@ description = "itertools and builtins for AsyncIO and mixed iterables" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aioitertools-0.12.0-py3-none-any.whl", hash = "sha256:fc1f5fac3d737354de8831cbba3eb04f79dd649d8f3afb4c5b114925e662a796"}, {file = "aioitertools-0.12.0.tar.gz", hash = "sha256:c2a9055b4fbb7705f561b9d86053e8af5d10cc845d22c32008c43490b2d8dd6b"}, @@ -180,7 +176,6 @@ description = "aiosignal: a list of registered asynchronous callbacks" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aiosignal-1.3.1-py3-none-any.whl", hash = "sha256:f8376fb07dd1e86a584e4fcdec80b36b7f81aac666ebc724e2c090300dd83b17"}, {file = "aiosignal-1.3.1.tar.gz", hash = "sha256:54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc"}, @@ -196,7 +191,7 @@ description = "A light, configurable Sphinx theme" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"}, {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"}, @@ -209,7 +204,6 @@ description = "A neighbour-joining library for Python." optional = false python-versions = "<3.13,>=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "anjl-1.4.0-py3-none-any.whl", hash = "sha256:062d9b6d3d565a61a0b691fa6ae1e268e28a9ef2271d12259c1b6d42b0a1abea"}, {file = "anjl-1.4.0.tar.gz", hash = "sha256:830d6b6233d3bc9cd5631da7a8ee798e348949a07429fae87e492659b5960fba"}, @@ -233,7 +227,7 @@ description = "High level compatibility layer for multiple asynchronous event lo optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "anyio-4.6.2.post1-py3-none-any.whl", hash = "sha256:6d170c36fba3bdd840c73d3868c1e777e33676a69c3a72cf0a0d5d6d8009b61d"}, {file = "anyio-4.6.2.post1.tar.gz", hash = "sha256:4c8bc31ccdb51c7f7bd251f51c609e038d63e34219b44aa86e47576389880b4c"}, @@ -247,7 +241,7 @@ typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21.0b1)"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1) ; python_version >= \"3.10\"", "uvloop (>=0.21.0b1) ; platform_python_implementation == \"CPython\" and platform_system != \"Windows\""] trio = ["trio (>=0.26.1)"] [[package]] @@ -257,7 +251,7 @@ description = "Disable App Nap on macOS >= 10.9" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and platform_system == \"Darwin\" or python_version >= \"3.12\" and platform_system == \"Darwin\"" +markers = "platform_system == \"Darwin\"" files = [ {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"}, {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"}, @@ -270,7 +264,7 @@ description = "Argon2 for Python" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "argon2_cffi-23.1.0-py3-none-any.whl", hash = "sha256:c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea"}, {file = "argon2_cffi-23.1.0.tar.gz", hash = "sha256:879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08"}, @@ -292,7 +286,7 @@ description = "Low-level CFFI bindings for Argon2" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "argon2-cffi-bindings-21.2.0.tar.gz", hash = "sha256:bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3"}, {file = "argon2_cffi_bindings-21.2.0-cp36-abi3-macosx_10_9_x86_64.whl", hash = "sha256:ccb949252cb2ab3a08c02024acb77cfb179492d5701c7cbdbfd776124d4d2367"}, @@ -331,7 +325,7 @@ description = "Better dates & times for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, @@ -352,7 +346,6 @@ description = "Draws ASCII trees." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "asciitree-0.3.3.tar.gz", hash = "sha256:4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e"}, ] @@ -364,7 +357,6 @@ description = "Annotate AST trees with source code positions" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"}, {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"}, @@ -381,7 +373,7 @@ description = "Simple LRU cache for asyncio" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "async-lru-2.0.4.tar.gz", hash = "sha256:b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627"}, {file = "async_lru-2.0.4-py3-none-any.whl", hash = "sha256:ff02944ce3c288c5be660c42dbcca0742b32c3b279d6dceda655190240b99224"}, @@ -397,7 +389,7 @@ description = "Timeout context manager for asyncio programs" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "async_timeout-5.0.1-py3-none-any.whl", hash = "sha256:39e3809566ff85354557ec2398b55e096c8364bacac9405a7a1fa429e77fe76c"}, {file = "async_timeout-5.0.1.tar.gz", hash = "sha256:d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3"}, @@ -410,19 +402,18 @@ description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, ] [package.extras] -benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"] +cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"] +dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"] docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"] -tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] +tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"] +tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\""] [[package]] name = "babel" @@ -431,7 +422,7 @@ description = "Internationalization utilities" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, @@ -447,7 +438,7 @@ description = "Screen-scraping library" optional = false python-versions = ">=3.6.0" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"}, {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"}, @@ -470,7 +461,6 @@ description = "Read and write the PLINK BED format, simply and efficiently." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "bed_reader-1.0.6-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:5f2e812dea71cf9aebbf8b1bf00149600948fdbf4bbdb8805c4a4ed4b1597aba"}, {file = "bed_reader-1.0.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:7753e3e9dcd4210aadfc071ece22264c4fef1bd53b31d34bd63ce11f217954d5"}, @@ -512,7 +502,6 @@ description = "Freely available tools for computational molecular biology." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:3c8beded38884abae4c74cb6ce54142da670273fd0b2919bd0f84f6e34d3056b"}, {file = "biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b51ef31bfb79872a182a85b4113625e1b553c024bb1586c72ac98b479f8d8fe4"}, @@ -551,7 +540,7 @@ description = "An easy safelist-based HTML-sanitizing tool." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"}, {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"}, @@ -570,7 +559,6 @@ description = "Fast, simple object-to-object and broadcast signaling" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "blinker-1.9.0-py3-none-any.whl", hash = "sha256:ba0efaa9080b619ff2f3459d1d500c57bddea4a6b424b60a91141db6fd2f08bc"}, {file = "blinker-1.9.0.tar.gz", hash = "sha256:b4ce2265a7abece45e7cc896e98dbebe6cead56bcf805a3d23136d145f5445bf"}, @@ -583,7 +571,6 @@ description = "Interactive plots and applications in the browser from Python" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "bokeh-3.6.2-py3-none-any.whl", hash = "sha256:fddc4b91f8b40178c0e3e83dfcc33886d7803a3a1f041a840834255e435a18c2"}, {file = "bokeh-3.6.2.tar.gz", hash = "sha256:2f3043d9ecb3d5dc2e8c0ebf8ad55727617188d4e534f3e7208b36357e352396"}, @@ -607,7 +594,6 @@ description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "botocore-1.35.36-py3-none-any.whl", hash = "sha256:64241c778bf2dc863d93abab159e14024d97a926a5715056ef6411418cb9ead3"}, {file = "botocore-1.35.36.tar.gz", hash = "sha256:354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797"}, @@ -628,7 +614,6 @@ description = "Generate complex HTML+JS pages with Python" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "branca-0.8.0-py3-none-any.whl", hash = "sha256:e78d5be39c8799a42e5c2dd1145a797a3cefc099537907bc1e4c43b6b55f7fa4"}, {file = "branca-0.8.0.tar.gz", hash = "sha256:1f8fd0d2f3b7548f2c146093932be5d3064ba21eee6cebf92d416b7f9092324f"}, @@ -644,7 +629,6 @@ description = "Extensible memoizing collections and decorators" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "cachetools-5.5.0-py3-none-any.whl", hash = "sha256:02134e8439cdc2ffb62023ce1debca2944c3f289d66bb17ead3ab3dede74b292"}, {file = "cachetools-5.5.0.tar.gz", hash = "sha256:2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a"}, @@ -657,7 +641,6 @@ description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"}, {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"}, @@ -670,7 +653,7 @@ description = "Foreign Function Interface for Python calling C code." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and implementation_name == \"pypy\" or python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and implementation_name == \"pypy\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "implementation_name == \"pypy\" or extra == \"dev\"" files = [ {file = "cffi-1.17.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:df8b1c11f177bc2313ec4b2d46baec87a5f3e71fc8b45dab2ee7cae86d9aba14"}, {file = "cffi-1.17.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8f2cdc858323644ab277e9bb925ad72ae0e67f69e804f4898c070998d50b1a67"}, @@ -751,7 +734,7 @@ description = "Validate configuration and produce human readable error messages. optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, @@ -764,7 +747,6 @@ description = "The Real First Universal Charset Detector. Open, modern and activ optional = false python-versions = ">=3.7.0" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:4f9fc98dad6c2eaa32fc3af1417d95b5e3d08aff968df0cd320066def971f9a6"}, {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0de7b687289d3c1b3e8660d0741874abe7888100efe14bd0f9fd7141bcbda92b"}, @@ -880,7 +862,6 @@ description = "Composable command line interface toolkit" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, @@ -896,7 +877,6 @@ description = "Pickler class to extend the standard pickle.Pickler functionality optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "cloudpickle-3.1.0-py3-none-any.whl", hash = "sha256:fe11acda67f61aaaec473e3afe030feb131d78a43461b718185363384f1ba12e"}, {file = "cloudpickle-3.1.0.tar.gz", hash = "sha256:81a929b6e3c7335c863c771d673d105f02efdb89dfaba0c90495d1c64796601b"}, @@ -909,7 +889,7 @@ description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" and platform_system == \"Windows\" or python_version <= \"3.11\" and sys_platform == \"win32\" or python_version >= \"3.12\" and platform_system == \"Windows\" or python_version >= \"3.12\" and sys_platform == \"win32\"" +markers = "platform_system == \"Windows\" or sys_platform == \"win32\"" files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, @@ -922,7 +902,6 @@ description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus- optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "comm-0.2.2-py3-none-any.whl", hash = "sha256:e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3"}, {file = "comm-0.2.2.tar.gz", hash = "sha256:3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e"}, @@ -941,7 +920,6 @@ description = "Python library for calculating contours of 2D quadrilateral grids optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "contourpy-1.3.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a045f341a77b77e1c5de31e74e966537bba9f3c4099b35bf4c2e3939dd54cdab"}, {file = "contourpy-1.3.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:500360b77259914f7805af7462e41f9cb7ca92ad38e9f94d6c8641b089338124"}, @@ -1016,7 +994,7 @@ description = "Code coverage measurement for Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "coverage-7.6.8-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b39e6011cd06822eb964d038d5dff5da5d98652b81f5ecd439277b32361a3a50"}, {file = "coverage-7.6.8-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:63c19702db10ad79151a059d2d6336fe0c470f2e18d0d4d1a57f7f9713875dcf"}, @@ -1086,7 +1064,7 @@ files = [ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""} [package.extras] -toml = ["tomli"] +toml = ["tomli ; python_full_version <= \"3.11.0a6\""] [[package]] name = "dash" @@ -1095,7 +1073,6 @@ description = "A Python framework for building reactive web-apps. Developed by P optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash-2.18.2-py3-none-any.whl", hash = "sha256:0ce0479d1bc958e934630e2de7023b8a4558f23ce1f9f5a4b34b65eb3903a869"}, {file = "dash-2.18.2.tar.gz", hash = "sha256:20e8404f73d0fe88ce2eae33c25bbc513cbe52f30d23a401fa5f24dbb44296c8"}, @@ -1130,7 +1107,6 @@ description = "Core component suite for Dash" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash_core_components-2.0.0-py3-none-any.whl", hash = "sha256:52b8e8cce13b18d0802ee3acbc5e888cb1248a04968f962d63d070400af2e346"}, {file = "dash_core_components-2.0.0.tar.gz", hash = "sha256:c6733874af975e552f95a1398a16c2ee7df14ce43fa60bb3718a3c6e0b63ffee"}, @@ -1143,7 +1119,6 @@ description = "A Component Library for Dash aimed at facilitating network visual optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash_cytoscape-1.0.2.tar.gz", hash = "sha256:a61019d2184d63a2b3b5c06d056d3b867a04223a674cc3c7cf900a561a9a59aa"}, ] @@ -1161,7 +1136,6 @@ description = "Vanilla HTML components for Dash" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash_html_components-2.0.0-py3-none-any.whl", hash = "sha256:b42cc903713c9706af03b3f2548bda4be7307a7cf89b7d6eae3da872717d1b63"}, {file = "dash_html_components-2.0.0.tar.gz", hash = "sha256:8703a601080f02619a6390998e0b3da4a5daabe97a1fd7a9cebc09d015f26e50"}, @@ -1174,7 +1148,6 @@ description = "Dash table" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash_table-5.0.0-py3-none-any.whl", hash = "sha256:19036fa352bb1c11baf38068ec62d172f0515f73ca3276c79dee49b95ddc16c9"}, {file = "dash_table-5.0.0.tar.gz", hash = "sha256:18624d693d4c8ef2ddec99a6f167593437a7ea0bf153aa20f318c170c5bc7308"}, @@ -1187,7 +1160,6 @@ description = "Parallel PyData with Task Scheduling" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dask-2024.12.0-py3-none-any.whl", hash = "sha256:e038e87b9f06e7927b81ecde6cf2b49aa699bb902fec11abba5697cb48baeb8d"}, {file = "dask-2024.12.0.tar.gz", hash = "sha256:ffd02b06ac06b993df0b48e0ba4fe02abceb5c8b34b40bd91d63f33ec7a272a4"}, @@ -1219,7 +1191,6 @@ description = "An implementation of the Debug Adapter Protocol for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "debugpy-1.8.9-cp310-cp310-macosx_14_0_x86_64.whl", hash = "sha256:cfe1e6c6ad7178265f74981edf1154ffce97b69005212fbc90ca22ddfe3d017e"}, {file = "debugpy-1.8.9-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ada7fb65102a4d2c9ab62e8908e9e9f12aed9d76ef44880367bc9308ebe49a0f"}, @@ -1256,7 +1227,7 @@ description = "Create decorators easily in python." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "decopatch-1.4.10-py2.py3-none-any.whl", hash = "sha256:e151f7f93de2b1b3fd3f3272dcc7cefd1a69f68ec1c2d8e288ecd9deb36dc5f7"}, {file = "decopatch-1.4.10.tar.gz", hash = "sha256:957f49c93f4150182c23f8fb51d13bb3213e0f17a79e09c8cca7057598b55720"}, @@ -1272,7 +1243,6 @@ description = "Decorators for Humans" optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"}, {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"}, @@ -1285,7 +1255,7 @@ description = "XML bomb protection for Python stdlib modules" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "defusedxml-0.7.1-py2.py3-none-any.whl", hash = "sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61"}, {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"}, @@ -1298,7 +1268,7 @@ description = "Distribution utilities" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "distlib-0.3.9-py2.py3-none-any.whl", hash = "sha256:47f8c22fd27c27e25a65601af709b38e4f0a45ea4fc2e710f65755fa8caaaf87"}, {file = "distlib-0.3.9.tar.gz", hash = "sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403"}, @@ -1311,7 +1281,6 @@ description = "Distributed scheduler for Dask" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "distributed-2024.12.0-py3-none-any.whl", hash = "sha256:ed05aa13b6c62b69b33d1ba7d1ca95e78406c8f37163fafd07f7ca94ae036b66"}, {file = "distributed-2024.12.0.tar.gz", hash = "sha256:6a2c04e63d31973ee3c1f2160d66521ed8f08e637d6a25a450e7561582920f38"}, @@ -1341,7 +1310,7 @@ description = "Docutils -- Python Documentation Utilities" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "docutils-0.21.2-py3-none-any.whl", hash = "sha256:dafca5b9e384f0e419294eb4d2ff9fa826435bf15f15b7bd45723e8ad76811b2"}, {file = "docutils-0.21.2.tar.gz", hash = "sha256:3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f"}, @@ -1354,7 +1323,7 @@ description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"}, {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"}, @@ -1370,7 +1339,7 @@ description = "execnet: rapid multi-Python deployment" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "execnet-2.1.1-py3-none-any.whl", hash = "sha256:26dee51f1b80cebd6d0ca8e74dd8745419761d3bef34163928cbebbdc4749fdc"}, {file = "execnet-2.1.1.tar.gz", hash = "sha256:5189b52c6121c24feae288166ab41b32549c7e2348652736540b9e6e7d4e72e3"}, @@ -1386,14 +1355,13 @@ description = "Get the currently executing AST node of a frame, and other inform optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "executing-2.1.0-py2.py3-none-any.whl", hash = "sha256:8d63781349375b5ebccc3142f4b30350c0cd9c79f921cde38be2be4637e98eaf"}, {file = "executing-2.1.0.tar.gz", hash = "sha256:8ea27ddd260da8150fa5a708269c4a10e76161e2496ec3e587da9e3c0fe4b9ab"}, ] [package.extras] -tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"] +tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich ; python_version >= \"3.11\""] [[package]] name = "fasteners" @@ -1402,7 +1370,7 @@ description = "A python package that provides useful locks" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and sys_platform != \"emscripten\" or python_version >= \"3.12\" and sys_platform != \"emscripten\"" +markers = "sys_platform != \"emscripten\"" files = [ {file = "fasteners-0.19-py3-none-any.whl", hash = "sha256:758819cb5d94cdedf4e836988b74de396ceacb8e2794d21f82d131fd9ee77237"}, {file = "fasteners-0.19.tar.gz", hash = "sha256:b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c"}, @@ -1415,7 +1383,7 @@ description = "Fastest Python implementation of JSON schema" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "fastjsonschema-2.21.1-py3-none-any.whl", hash = "sha256:c9e5b7e908310918cf494a434eeb31384dd84a98b57a30bcb1f535015b554667"}, {file = "fastjsonschema-2.21.1.tar.gz", hash = "sha256:794d4f0a58f848961ba16af7b9c85a3e88cd360df008c59aac6fc5ae9323b5d4"}, @@ -1431,7 +1399,7 @@ description = "A platform independent file lock." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "filelock-3.16.1-py3-none-any.whl", hash = "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0"}, {file = "filelock-3.16.1.tar.gz", hash = "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435"}, @@ -1440,7 +1408,7 @@ files = [ [package.extras] docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4.1)"] testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"] -typing = ["typing-extensions (>=4.12.2)"] +typing = ["typing-extensions (>=4.12.2) ; python_version < \"3.11\""] [[package]] name = "flask" @@ -1449,7 +1417,6 @@ description = "A simple framework for building complex web applications." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "flask-3.0.3-py3-none-any.whl", hash = "sha256:34e815dfaa43340d1d15a5c3a02b8476004037eb4840b34910c6e21679d288f3"}, {file = "flask-3.0.3.tar.gz", hash = "sha256:ceb27b0af3823ea2737928a4d99d125a06175b8512c445cbd9a9ce200ef76842"}, @@ -1473,7 +1440,7 @@ description = "Validates fully-qualified domain names against RFC 1123, so that optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"}, {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"}, @@ -1486,7 +1453,6 @@ description = "A list-like structure which implements collections.abc.MutableSeq optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "frozenlist-1.5.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:5b6a66c18b5b9dd261ca98dffcb826a525334b2f29e7caa54e182255c5f6a65a"}, {file = "frozenlist-1.5.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d1b3eb7b05ea246510b43a7e53ed1653e55c2121019a97e60cad7efb881a97bb"}, @@ -1589,7 +1555,6 @@ description = "File-system specification" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "fsspec-2024.10.0-py3-none-any.whl", hash = "sha256:03b9a6785766a4de40368b88906366755e2819e758b83705c88cd7cb5fe81871"}, {file = "fsspec-2024.10.0.tar.gz", hash = "sha256:eda2d8a4116d4f2429db8550f2457da57279247dd930bb12f821b58391359493"}, @@ -1630,7 +1595,6 @@ description = "Convenient Filesystem interface over GCS" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "gcsfs-2024.10.0-py2.py3-none-any.whl", hash = "sha256:bb2d23547e61203ea2dda5fa6c4b91a0c34b74ebe8bb6ab1926f6c33381bceb2"}, {file = "gcsfs-2024.10.0.tar.gz", hash = "sha256:5df54cfe568e8fdeea5aafa7fed695cdc69a9a674e991ca8c1ce634f5df1d314"}, @@ -1656,7 +1620,6 @@ description = "Google API client core library" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_api_core-2.23.0-py3-none-any.whl", hash = "sha256:c20100d4c4c41070cf365f1d8ddf5365915291b5eb11b83829fbd1c999b5122f"}, {file = "google_api_core-2.23.0.tar.gz", hash = "sha256:2ceb087315e6af43f256704b871d99326b1f12a9d6ce99beaedec99ba26a0ace"}, @@ -1671,7 +1634,7 @@ requests = ">=2.18.0,<3.0.0.dev0" [package.extras] async-rest = ["google-auth[aiohttp] (>=2.35.0,<3.0.dev0)"] -grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio (>=1.49.1,<2.0dev)", "grpcio-status (>=1.33.2,<2.0.dev0)", "grpcio-status (>=1.49.1,<2.0.dev0)"] +grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio (>=1.49.1,<2.0dev) ; python_version >= \"3.11\"", "grpcio-status (>=1.33.2,<2.0.dev0)", "grpcio-status (>=1.49.1,<2.0.dev0) ; python_version >= \"3.11\""] grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] @@ -1682,7 +1645,6 @@ description = "Google Authentication Library" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_auth-2.36.0-py2.py3-none-any.whl", hash = "sha256:51a15d47028b66fd36e5c64a82d2d57480075bccc7da37cde257fc94177a61fb"}, {file = "google_auth-2.36.0.tar.gz", hash = "sha256:545e9618f2df0bcbb7dcbc45a546485b1212624716975a1ea5ae8149ce769ab1"}, @@ -1707,7 +1669,6 @@ description = "Google Authentication Library" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_auth_oauthlib-1.2.1-py2.py3-none-any.whl", hash = "sha256:2d58a27262d55aa1b87678c3ba7142a080098cbc2024f903c62355deb235d91f"}, {file = "google_auth_oauthlib-1.2.1.tar.gz", hash = "sha256:afd0cad092a2eaa53cd8e8298557d6de1034c6cb4a740500b5357b648af97263"}, @@ -1727,7 +1688,6 @@ description = "Google Cloud API client core library" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google-cloud-core-2.4.1.tar.gz", hash = "sha256:9b7749272a812bde58fff28868d0c5e2f585b82f37e09a1f6ed2d4d10f134073"}, {file = "google_cloud_core-2.4.1-py2.py3-none-any.whl", hash = "sha256:a9e6a4422b9ac5c29f79a0ede9485473338e2ce78d91f2370c01e730eab22e61"}, @@ -1747,7 +1707,6 @@ description = "Google Cloud Storage API client library" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_cloud_storage-2.18.2-py2.py3-none-any.whl", hash = "sha256:97a4d45c368b7d401ed48c4fdfe86e1e1cb96401c9e199e419d289e2c0370166"}, {file = "google_cloud_storage-2.18.2.tar.gz", hash = "sha256:aaf7acd70cdad9f274d29332673fcab98708d0e1f4dceb5a5356aaef06af4d99"}, @@ -1772,7 +1731,6 @@ description = "A python wrapper of the C library 'Google CRC32C'" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_crc32c-1.6.0-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:5bcc90b34df28a4b38653c36bb5ada35671ad105c99cfe915fb5bed7ad6924aa"}, {file = "google_crc32c-1.6.0-cp310-cp310-macosx_12_0_x86_64.whl", hash = "sha256:d9e9913f7bd69e093b81da4535ce27af842e7bf371cde42d1ae9e9bd382dc0e9"}, @@ -1813,7 +1771,6 @@ description = "Utilities for Google Media Downloads and Resumable Uploads" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_resumable_media-2.7.2-py2.py3-none-any.whl", hash = "sha256:3ce7551e9fe6d99e9a126101d2536612bb73486721951e9562fee0f90c6ababa"}, {file = "google_resumable_media-2.7.2.tar.gz", hash = "sha256:5280aed4629f2b60b847b0d42f9857fd4935c11af266744df33d8074cae92fe0"}, @@ -1833,7 +1790,6 @@ description = "Common protobufs used in Google APIs" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "googleapis_common_protos-1.66.0-py2.py3-none-any.whl", hash = "sha256:d7abcd75fabb2e0ec9f74466401f6c119a0b498e27370e9be4c94cb7e382b8ed"}, {file = "googleapis_common_protos-1.66.0.tar.gz", hash = "sha256:c3e7b33d15fdca5374cc0a7346dd92ffa847425cc4ea941d970f13680052ec8c"}, @@ -1852,7 +1808,7 @@ description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "h11-0.14.0-py3-none-any.whl", hash = "sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761"}, {file = "h11-0.14.0.tar.gz", hash = "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d"}, @@ -1865,7 +1821,7 @@ description = "A minimal low-level HTTP client." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "httpcore-1.0.7-py3-none-any.whl", hash = "sha256:a3fff8f43dc260d5bd363d9f9cf1830fa3a458b332856f34282de498ed420edd"}, {file = "httpcore-1.0.7.tar.gz", hash = "sha256:8551cb62a169ec7162ac7be8d4817d561f60e08eaa485234898414bb5a8a0b4c"}, @@ -1888,7 +1844,7 @@ description = "The next generation HTTP client." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "httpx-0.28.0-py3-none-any.whl", hash = "sha256:dc0b419a0cfeb6e8b34e85167c0da2671206f5095f1baa9663d23bcfd6b535fc"}, {file = "httpx-0.28.0.tar.gz", hash = "sha256:0858d3bab51ba7e386637f22a61d8ccddaeec5f3fe4209da3a6168dbb91573e0"}, @@ -1901,7 +1857,7 @@ httpcore = "==1.*" idna = "*" [package.extras] -brotli = ["brotli", "brotlicffi"] +brotli = ["brotli ; platform_python_implementation == \"CPython\"", "brotlicffi ; platform_python_implementation != \"CPython\""] cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"] http2 = ["h2 (>=3,<5)"] socks = ["socksio (==1.*)"] @@ -1914,7 +1870,7 @@ description = "File identification library for Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "identify-2.6.3-py2.py3-none-any.whl", hash = "sha256:9edba65473324c2ea9684b1f944fe3191db3345e50b6d04571d10ed164f8d7bd"}, {file = "identify-2.6.3.tar.gz", hash = "sha256:62f5dae9b5fef52c84cc188514e9ea4f3f636b1d8799ab5ebc475471f9e47a02"}, @@ -1930,7 +1886,6 @@ description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"}, {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"}, @@ -1946,7 +1901,6 @@ description = "Package for embedding the igv.js genome visualization in IPython optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "igv-notebook-0.6.1.tar.gz", hash = "sha256:37e4f091d93536775c99075b7fac11069186e22f05874dd2da886b7dc09e9e0d"}, {file = "igv_notebook-0.6.1-py3-none-any.whl", hash = "sha256:e13a53d245d6d51603173fbdd481f051344d79cbaeaa69f4bcc569a1c5387559"}, @@ -1964,7 +1918,7 @@ description = "Getting image size from png/jpeg/jpeg2000/gif file" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"}, {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"}, @@ -1977,7 +1931,6 @@ description = "Read metadata from Python packages" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "importlib_metadata-8.5.0-py3-none-any.whl", hash = "sha256:45e54197d28b7a7f1559e60b95e7c567032b602131fbd588f1497f47880aa68b"}, {file = "importlib_metadata-8.5.0.tar.gz", hash = "sha256:71522656f0abace1d072b9e5481a48f07c138e00f079c38c8f883823f9c26bd7"}, @@ -1987,12 +1940,12 @@ files = [ zipp = ">=3.20" [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] perf = ["ipython"] -test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] +test = ["flufl.flake8", "importlib-resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] type = ["pytest-mypy"] [[package]] @@ -2002,7 +1955,7 @@ description = "brain-dead simple config-ini parsing" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, @@ -2015,7 +1968,6 @@ description = "Official Python library for IPInfo" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipinfo-5.1.1-py3-none-any.whl", hash = "sha256:90b2f5400189dd2da7625c9151d7076879a8cac9c31bfb581689345fac34cceb"}, {file = "ipinfo-5.1.1.tar.gz", hash = "sha256:be5a33adac9681bc68280eb5aae16a83e4abbb5f192c87dcc5ee18bdd0ceb276"}, @@ -2033,7 +1985,6 @@ description = "IPython Kernel for Jupyter" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipykernel-6.29.5-py3-none-any.whl", hash = "sha256:afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5"}, {file = "ipykernel-6.29.5.tar.gz", hash = "sha256:f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215"}, @@ -2068,7 +2019,6 @@ description = "A Jupyter widget for dynamic Leaflet maps" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipyleaflet-0.19.2-py3-none-any.whl", hash = "sha256:7cc9157848baca2e1793b96e79f8bdb1aa7340521d2b7d8a62aa8bc30eab5278"}, {file = "ipyleaflet-0.19.2.tar.gz", hash = "sha256:b3b83fe3460e742964c2a5924ea7934365a3749bb75310ce388d45fd751372d2"}, @@ -2088,7 +2038,6 @@ description = "IPython: Productive Interactive Computing" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipython-8.30.0-py3-none-any.whl", hash = "sha256:85ec56a7e20f6c38fce7727dcca699ae4ffc85985aa7b23635a8008f918ae321"}, {file = "ipython-8.30.0.tar.gz", hash = "sha256:cb0a405a306d2995a5cbb9901894d240784a9f341394c6ba3f4fe8c6eb89ff6e"}, @@ -2110,7 +2059,7 @@ typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""} [package.extras] all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"] black = ["black"] -doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing_extensions"] +doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli ; python_version < \"3.11\"", "typing_extensions"] kernel = ["ipykernel"] matplotlib = ["matplotlib"] nbconvert = ["nbconvert"] @@ -2128,7 +2077,6 @@ description = "Jupyter interactive widgets" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipywidgets-8.1.5-py3-none-any.whl", hash = "sha256:3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245"}, {file = "ipywidgets-8.1.5.tar.gz", hash = "sha256:870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17"}, @@ -2151,7 +2099,7 @@ description = "Operations with ISO 8601 durations" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"}, {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"}, @@ -2167,7 +2115,6 @@ description = "Safely pass data to untrusted environments and back." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "itsdangerous-2.2.0-py3-none-any.whl", hash = "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef"}, {file = "itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173"}, @@ -2180,7 +2127,6 @@ description = "An autocompletion tool for Python that can be used for text edito optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"}, {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"}, @@ -2201,7 +2147,6 @@ description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"}, {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"}, @@ -2220,7 +2165,6 @@ description = "JSON Matching Expressions" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jmespath-1.0.1-py3-none-any.whl", hash = "sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980"}, {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"}, @@ -2233,7 +2177,6 @@ description = "Lightweight pipelining with Python functions" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"}, {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"}, @@ -2246,7 +2189,7 @@ description = "A Python implementation of the JSON5 data format." optional = false python-versions = ">=3.8.0" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "json5-0.10.0-py3-none-any.whl", hash = "sha256:19b23410220a7271e8377f81ba8aacba2fdd56947fbb137ee5977cbe1f5e8dfa"}, {file = "json5-0.10.0.tar.gz", hash = "sha256:e66941c8f0a02026943c52c2eb34ebeb2a6f819a0be05920a6f5243cd30fd559"}, @@ -2262,7 +2205,7 @@ description = "Identify specific nodes in a JSON document (RFC 6901)" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942"}, {file = "jsonpointer-3.0.0.tar.gz", hash = "sha256:2b2d729f2091522d61c3b31f82e11870f60b68f43fbc705cb76bf4b832af59ef"}, @@ -2275,7 +2218,7 @@ description = "An implementation of JSON Schema validation for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"}, {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"}, @@ -2306,7 +2249,7 @@ description = "The JSON Schema meta-schemas and vocabularies, exposed as a Regis optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jsonschema_specifications-2024.10.1-py3-none-any.whl", hash = "sha256:a09a0680616357d9a0ecf05c12ad234479f549239d0f5b55f3deea67475da9bf"}, {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"}, @@ -2322,7 +2265,6 @@ description = "Jupyter protocol implementation and client libraries" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"}, {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"}, @@ -2337,7 +2279,7 @@ traitlets = ">=5.3" [package.extras] docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] -test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"] +test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko ; sys_platform == \"win32\"", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"] [[package]] name = "jupyter-core" @@ -2346,7 +2288,6 @@ description = "Jupyter core package. A base package on which Jupyter projects re optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"}, {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"}, @@ -2368,7 +2309,7 @@ description = "Jupyter Event System library" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyter_events-0.10.0-py3-none-any.whl", hash = "sha256:4b72130875e59d57716d327ea70d3ebc3af1944d3717e5a498b8a06c6c159960"}, {file = "jupyter_events-0.10.0.tar.gz", hash = "sha256:670b8229d3cc882ec782144ed22e0d29e1c2d639263f92ca8383e66682845e22"}, @@ -2395,7 +2336,6 @@ description = "ipyleaflet extensions for JupyterLab and Jupyter Notebook" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_leaflet-0.19.2-py3-none-any.whl", hash = "sha256:0d57e15e80c08a4360f0cde0b4c490beddc5d422bb0e9bc1c0b4479d3fb725a6"}, {file = "jupyter_leaflet-0.19.2.tar.gz", hash = "sha256:b09b5ba48b1488cb61da37a6f558347269eb53ff6d64dc1a73e005ffc4420063"}, @@ -2408,7 +2348,7 @@ description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab se optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"}, {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"}, @@ -2424,7 +2364,7 @@ description = "The backend—i.e. core services, APIs, and REST endpoints—to J optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"}, {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"}, @@ -2462,7 +2402,7 @@ description = "A Jupyter Server Extension Providing Terminals." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyter_server_terminals-0.5.3-py3-none-any.whl", hash = "sha256:41ee0d7dc0ebf2809c668e0fc726dfaf258fcd3e769568996ca731b6194ae9aa"}, {file = "jupyter_server_terminals-0.5.3.tar.gz", hash = "sha256:5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269"}, @@ -2483,7 +2423,7 @@ description = "JupyterLab computational environment" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyterlab-4.3.2-py3-none-any.whl", hash = "sha256:e87100cbab8b886ff7a4f325c856100ba6fdfe916162a85409daf0e707e19d1d"}, {file = "jupyterlab-4.3.2.tar.gz", hash = "sha256:3c0a6882dbddcc0a7bfdd5e2236f351b2b263e48780236e6996c2aca13ac5b22"}, @@ -2519,7 +2459,7 @@ description = "Pygments theme using JupyterLab CSS variables" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyterlab_pygments-0.3.0-py3-none-any.whl", hash = "sha256:841a89020971da1d8693f1a99997aefc5dc424bb1b251fd6322462a1b8842780"}, {file = "jupyterlab_pygments-0.3.0.tar.gz", hash = "sha256:721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d"}, @@ -2532,7 +2472,7 @@ description = "A set of server components for JupyterLab and JupyterLab like app optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyterlab_server-2.27.3-py3-none-any.whl", hash = "sha256:e697488f66c3db49df675158a77b3b017520d772c6e1548c7d9bcc5df7944ee4"}, {file = "jupyterlab_server-2.27.3.tar.gz", hash = "sha256:eb36caca59e74471988f0ae25c77945610b887f777255aa21f8065def9e51ed4"}, @@ -2559,7 +2499,6 @@ description = "Jupyter interactive widgets for JupyterLab" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyterlab_widgets-3.0.13-py3-none-any.whl", hash = "sha256:e3cda2c233ce144192f1e29914ad522b2f4c40e77214b0cc97377ca3d323db54"}, {file = "jupyterlab_widgets-3.0.13.tar.gz", hash = "sha256:a2966d385328c1942b683a8cd96b89b8dd82c8b8f81dda902bb2bc06d46f5bed"}, @@ -2572,7 +2511,6 @@ description = "lightweight wrapper around basic LLVM functionality" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "llvmlite-0.43.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a289af9a1687c6cf463478f0fa8e8aa3b6fb813317b0d70bf1ed0759eab6f761"}, {file = "llvmlite-0.43.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6d4fd101f571a31acb1559ae1af30f30b1dc4b3186669f92ad780e17c81e91bc"}, @@ -2604,7 +2542,6 @@ description = "File-based locks for Python on Linux and Windows" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "locket-1.0.0-py2.py3-none-any.whl", hash = "sha256:b6c819a722f7b6bd955b80781788e4a66a55628b858d347536b7e81325a3a5e3"}, {file = "locket-1.0.0.tar.gz", hash = "sha256:5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632"}, @@ -2617,7 +2554,7 @@ description = "Small library to dynamically create python functions." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "makefun-1.15.6-py2.py3-none-any.whl", hash = "sha256:e69b870f0bb60304765b1e3db576aaecf2f9b3e5105afe8cfeff8f2afe6ad067"}, {file = "makefun-1.15.6.tar.gz", hash = "sha256:26bc63442a6182fb75efed8b51741dd2d1db2f176bec8c64e20a586256b8f149"}, @@ -2630,7 +2567,6 @@ description = "Safely add untrusted strings to HTML/XML markup." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7e94c425039cde14257288fd61dcfb01963e658efbc0ff54f5306b06054700f8"}, {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9e2d922824181480953426608b81967de705c3cef4d1af983af849d7bd619158"}, @@ -2702,7 +2638,6 @@ description = "Inline Matplotlib backend for Jupyter" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "matplotlib_inline-0.1.7-py3-none-any.whl", hash = "sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca"}, {file = "matplotlib_inline-0.1.7.tar.gz", hash = "sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90"}, @@ -2718,7 +2653,7 @@ description = "A module for monitoring memory usage of a python program" optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "memory_profiler-0.61.0-py3-none-any.whl", hash = "sha256:400348e61031e3942ad4d4109d18753b2fb08c2f6fb8290671c5513a34182d84"}, {file = "memory_profiler-0.61.0.tar.gz", hash = "sha256:4e5b73d7864a1d1292fb76a03e82a3e78ef934d06828a698d9dada76da2067b0"}, @@ -2734,7 +2669,7 @@ description = "A sane and fast Markdown parser with useful plugins and renderers optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "mistune-3.0.2-py3-none-any.whl", hash = "sha256:71481854c30fdbc938963d3605b72501f5c10a9320ecd412c121c163a1c7d205"}, {file = "mistune-3.0.2.tar.gz", hash = "sha256:fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8"}, @@ -2747,7 +2682,6 @@ description = "MessagePack serializer" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "msgpack-1.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7ad442d527a7e358a469faf43fda45aaf4ac3249c8310a82f0ccff9164e5dccd"}, {file = "msgpack-1.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:74bed8f63f8f14d75eec75cf3d04ad581da6b914001b474a5d3cd3372c8cc27d"}, @@ -2822,7 +2756,6 @@ description = "multidict implementation" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "multidict-6.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3380252550e372e8511d49481bd836264c009adb826b23fefcc5dd3c69692f60"}, {file = "multidict-6.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:99f826cbf970077383d7de805c0681799491cb939c25450b9b5b3ced03ca99f1"}, @@ -2928,7 +2861,7 @@ description = "Optional static typing for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "mypy-1.13.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6607e0f1dd1fb7f0aca14d936d13fd19eba5e17e1cd2a14f808fa5f8f6d8f60a"}, {file = "mypy-1.13.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8a21be69bd26fa81b1f80a61ee7ab05b076c674d9b18fb56239d72e21d9f4c80"}, @@ -2983,7 +2916,7 @@ description = "Type system extensions for programs checked with the mypy type ch optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"}, {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"}, @@ -2996,7 +2929,7 @@ description = "A client library for executing notebooks. Formerly nbconvert's Ex optional = false python-versions = ">=3.8.0" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "nbclient-0.10.1-py3-none-any.whl", hash = "sha256:949019b9240d66897e442888cfb618f69ef23dc71c01cb5fced8499c2cfc084d"}, {file = "nbclient-0.10.1.tar.gz", hash = "sha256:3e93e348ab27e712acd46fccd809139e356eb9a31aab641d1a7991a6eb4e6f68"}, @@ -3020,7 +2953,7 @@ description = "Converting Jupyter Notebooks (.ipynb files) to other formats. Ou optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "nbconvert-7.16.4-py3-none-any.whl", hash = "sha256:05873c620fe520b6322bf8a5ad562692343fe3452abda5765c7a34b7d1aa3eb3"}, {file = "nbconvert-7.16.4.tar.gz", hash = "sha256:86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4"}, @@ -3059,7 +2992,7 @@ description = "The Jupyter Notebook format" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "nbformat-5.10.4-py3-none-any.whl", hash = "sha256:3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b"}, {file = "nbformat-5.10.4.tar.gz", hash = "sha256:322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a"}, @@ -3082,7 +3015,6 @@ description = "Patch asyncio to allow nested event loops" optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "nest_asyncio-1.6.0-py3-none-any.whl", hash = "sha256:87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c"}, {file = "nest_asyncio-1.6.0.tar.gz", hash = "sha256:6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe"}, @@ -3095,7 +3027,6 @@ description = "Python package for creating and manipulating graphs and networks" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "networkx-3.4.2-py3-none-any.whl", hash = "sha256:df5d4365b724cf81b8c6a7312509d0c22386097011ad1abe274afd5e9d3bbc5f"}, {file = "networkx-3.4.2.tar.gz", hash = "sha256:307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1"}, @@ -3116,7 +3047,7 @@ description = "Node.js virtual environment builder" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"}, {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"}, @@ -3129,7 +3060,7 @@ description = "Jupyter Notebook - A web-based notebook environment for interacti optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "notebook-7.3.0-py3-none-any.whl", hash = "sha256:affa2fdbc10661aa05790ba105836871666b3919559abb5bc92dd8d9f0cbeee3"}, {file = "notebook-7.3.0.tar.gz", hash = "sha256:e1dc37db32620b04043ae78866a40b087c43308d85067699db99e6f9e22846bc"}, @@ -3145,7 +3076,7 @@ tornado = ">=6.2.0" [package.extras] dev = ["hatch", "pre-commit"] docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] -test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.27.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"] +test = ["importlib-resources (>=5.0) ; python_version < \"3.10\"", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.27.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"] [[package]] name = "notebook-shim" @@ -3154,7 +3085,7 @@ description = "A shim layer for notebook traits and config" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "notebook_shim-0.2.4-py3-none-any.whl", hash = "sha256:411a5be4e9dc882a074ccbcae671eda64cceb068767e9a3419096986560e1cef"}, {file = "notebook_shim-0.2.4.tar.gz", hash = "sha256:b4b2cfa1b65d98307ca24361f5b30fe785b53c3fd07b7a47e89acb5e6ac638cb"}, @@ -3173,7 +3104,6 @@ description = "compiling Python code using LLVM" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "numba-0.60.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5d761de835cd38fb400d2c26bb103a2726f548dc30368853121d66201672e651"}, {file = "numba-0.60.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:159e618ef213fba758837f9837fb402bbe65326e60ba0633dbe6c7f274d42c1b"}, @@ -3209,7 +3139,6 @@ description = "A Python package providing buffer compression and transformation optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "numcodecs-0.13.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:96add4f783c5ce57cc7e650b6cac79dd101daf887c479a00a29bc1487ced180b"}, {file = "numcodecs-0.13.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:237b7171609e868a20fd313748494444458ccd696062f67e198f7f8f52000c15"}, @@ -3248,7 +3177,6 @@ description = "Fundamental package for array computing in Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "numpy-2.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:51129a29dbe56f9ca83438b706e2e69a39892b5eda6cedcb6b0c9fdc9b0d3ece"}, {file = "numpy-2.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:f15975dfec0cf2239224d80e32c3170b1d168335eaedee69da84fbe9f1f9cd04"}, @@ -3304,7 +3232,6 @@ description = "" optional = false python-versions = "<3.13,>=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "numpydoc_decorator-2.2.1-py3-none-any.whl", hash = "sha256:16181c97b20c2099d6fd75404bef379cc3678338d9aa8e6e8fafb3ae7adc166a"}, {file = "numpydoc_decorator-2.2.1.tar.gz", hash = "sha256:c3b5b16bec1e7ed221adab7bd77a8a8acc0c7be1bb4e0871721b2a5d2f3145fa"}, @@ -3320,7 +3247,6 @@ description = "A generic, spec-compliant, thorough implementation of the OAuth r optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "oauthlib-3.2.2-py3-none-any.whl", hash = "sha256:8139f29aac13e25d502680e9e19963e83f16838d48a0d71c287fe40e7067fbca"}, {file = "oauthlib-3.2.2.tar.gz", hash = "sha256:9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918"}, @@ -3338,7 +3264,6 @@ description = "Fast, correct Python JSON library supporting dataclasses, datetim optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "orjson-3.10.12-cp310-cp310-macosx_10_15_x86_64.macosx_11_0_arm64.macosx_10_15_universal2.whl", hash = "sha256:ece01a7ec71d9940cc654c482907a6b65df27251255097629d0dea781f255c6d"}, {file = "orjson-3.10.12-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c34ec9aebc04f11f4b978dd6caf697a2df2dd9b47d35aa4cc606cabcb9df69d7"}, @@ -3424,7 +3349,7 @@ description = "A decorator to automatically detect mismatch when overriding a me optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "overrides-7.7.0-py3-none-any.whl", hash = "sha256:c7ed9d062f78b8e4c1a7b70bd8796b35ead4d9f510227ef9c5dc7626c60d7e49"}, {file = "overrides-7.7.0.tar.gz", hash = "sha256:55158fa3d93b98cc75299b1e67078ad9003ca27945c76162c1c0766d6f91820a"}, @@ -3437,7 +3362,6 @@ description = "Core utilities for Python packages" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "packaging-24.2-py3-none-any.whl", hash = "sha256:09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759"}, {file = "packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"}, @@ -3450,7 +3374,6 @@ description = "Powerful data structures for data analysis, time series, and stat optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1948ddde24197a0f7add2bdc4ca83bf2b1ef84a1bc8ccffd95eda17fd836ecb5"}, {file = "pandas-2.2.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:381175499d3802cde0eabbaf6324cce0c4f5d52ca6f8c377c29ad442f50f6348"}, @@ -3538,7 +3461,7 @@ description = "Type annotations for pandas" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pandas_stubs-2.2.3.241126-py3-none-any.whl", hash = "sha256:74aa79c167af374fe97068acc90776c0ebec5266a6e5c69fe11e9c2cf51f2267"}, {file = "pandas_stubs-2.2.3.241126.tar.gz", hash = "sha256:cf819383c6d9ae7d4dabf34cd47e1e45525bb2f312e6ad2939c2c204cb708acd"}, @@ -3555,7 +3478,7 @@ description = "Utilities for writing pandoc filters in python" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pandocfilters-1.5.1-py2.py3-none-any.whl", hash = "sha256:93be382804a9cdb0a7267585f157e5d1731bbe5545a85b268d6f5fe6232de2bc"}, {file = "pandocfilters-1.5.1.tar.gz", hash = "sha256:002b4a555ee4ebc03f8b66307e287fa492e4a77b4ea14d3f934328297bb4939e"}, @@ -3568,7 +3491,6 @@ description = "A Python Parser" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "parso-0.8.4-py2.py3-none-any.whl", hash = "sha256:a418670a20291dacd2dddc80c377c5c3791378ee1e8d12bffc35420643d43f18"}, {file = "parso-0.8.4.tar.gz", hash = "sha256:eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d"}, @@ -3585,7 +3507,6 @@ description = "Appendable key-value storage" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "partd-1.4.2-py3-none-any.whl", hash = "sha256:978e4ac767ec4ba5b86c6eaa52e5a2a3bc748a2ca839e8cc798f1cc6ce6efb0f"}, {file = "partd-1.4.2.tar.gz", hash = "sha256:d022c33afbdc8405c226621b015e8067888173d85f7f5ecebb3cafed9a20f02c"}, @@ -3605,7 +3526,6 @@ description = "A Python package for describing statistical models and for buildi optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "patsy-1.0.1-py2.py3-none-any.whl", hash = "sha256:751fb38f9e97e62312e921a1954b81e1bb2bcda4f5eeabaf94db251ee791509c"}, {file = "patsy-1.0.1.tar.gz", hash = "sha256:e786a9391eec818c054e359b737bbce692f051aee4c661f4141cc88fb459c0c4"}, @@ -3624,7 +3544,7 @@ description = "Pexpect allows easy control of interactive console applications." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and (sys_platform != \"win32\" and sys_platform != \"emscripten\") or python_version >= \"3.12\" and (sys_platform != \"win32\" and sys_platform != \"emscripten\")" +markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\"" files = [ {file = "pexpect-4.9.0-py2.py3-none-any.whl", hash = "sha256:7236d1e080e4936be2dc3e326cec0af72acf9212a7e1d060210e70a47e253523"}, {file = "pexpect-4.9.0.tar.gz", hash = "sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"}, @@ -3640,7 +3560,6 @@ description = "Python Imaging Library (Fork)" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pillow-11.0.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:6619654954dc4936fcff82db8eb6401d3159ec6be81e33c6000dfd76ae189947"}, {file = "pillow-11.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b3c5ac4bed7519088103d9450a1107f76308ecf91d6dabc8a33a2fcfb18d0fba"}, @@ -3724,7 +3643,7 @@ docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline fpx = ["olefile"] mic = ["olefile"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] -typing = ["typing-extensions"] +typing = ["typing-extensions ; python_version < \"3.10\""] xmp = ["defusedxml"] [[package]] @@ -3734,7 +3653,6 @@ description = "A small Python package for determining appropriate platform-speci optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "platformdirs-4.3.6-py3-none-any.whl", hash = "sha256:73e575e1408ab8103900836b97580d5307456908a03e92031bab39e4554cc3fb"}, {file = "platformdirs-4.3.6.tar.gz", hash = "sha256:357fb2acbc885b0419afd3ce3ed34564c13c9b95c89360cd9563f73aa5e2b907"}, @@ -3752,7 +3670,6 @@ description = "An open-source, interactive data visualization library for Python optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "plotly-5.24.1-py3-none-any.whl", hash = "sha256:f67073a1e637eb0dc3e46324d9d51e2fe76e9727c892dde64ddf1e1b51f29089"}, {file = "plotly-5.24.1.tar.gz", hash = "sha256:dbc8ac8339d248a4bcc36e08a5659bacfe1b079390b8953533f4eb22169b4bae"}, @@ -3769,7 +3686,7 @@ description = "plugin and hook calling mechanisms for python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"}, {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"}, @@ -3786,7 +3703,7 @@ description = "A framework for managing and maintaining multi-language pre-commi optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pre_commit-4.0.1-py2.py3-none-any.whl", hash = "sha256:efde913840816312445dc98787724647c65473daefe420785f885e8ed9a06878"}, {file = "pre_commit-4.0.1.tar.gz", hash = "sha256:80905ac375958c0444c65e9cebebd948b3cdb518f335a091a670a89d652139d2"}, @@ -3806,7 +3723,7 @@ description = "Python client for the Prometheus monitoring system." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "prometheus_client-0.21.1-py3-none-any.whl", hash = "sha256:594b45c410d6f4f8888940fe80b5cc2521b305a1fafe1c58609ef715a001f301"}, {file = "prometheus_client-0.21.1.tar.gz", hash = "sha256:252505a722ac04b0456be05c05f75f45d760c2911ffc45f2a06bcaed9f3ae3fb"}, @@ -3822,7 +3739,6 @@ description = "Library for building powerful interactive command lines in Python optional = false python-versions = ">=3.7.0" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "prompt_toolkit-3.0.48-py3-none-any.whl", hash = "sha256:f49a827f90062e411f1ce1f854f2aedb3c23353244f8108b89283587397ac10e"}, {file = "prompt_toolkit-3.0.48.tar.gz", hash = "sha256:d6623ab0477a80df74e646bdbc93621143f5caf104206aa29294d53de1a03d90"}, @@ -3838,7 +3754,6 @@ description = "Accelerated property cache" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "propcache-0.2.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:6b3f39a85d671436ee3d12c017f8fdea38509e4f25b28eb25877293c98c243f6"}, {file = "propcache-0.2.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:39d51fbe4285d5db5d92a929e3e21536ea3dd43732c5b177c7ef03f918dff9f2"}, @@ -3931,7 +3846,6 @@ description = "Beautiful, Pythonic protocol buffers." optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "proto_plus-1.25.0-py3-none-any.whl", hash = "sha256:c91fc4a65074ade8e458e95ef8bac34d4008daa7cce4a12d6707066fca648961"}, {file = "proto_plus-1.25.0.tar.gz", hash = "sha256:fbb17f57f7bd05a68b7707e745e26528b0b3c34e378db91eef93912c54982d91"}, @@ -3950,7 +3864,6 @@ description = "" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "protobuf-5.29.0-cp310-abi3-win32.whl", hash = "sha256:ea7fb379b257911c8c020688d455e8f74efd2f734b72dc1ea4b4d7e9fd1326f2"}, {file = "protobuf-5.29.0-cp310-abi3-win_amd64.whl", hash = "sha256:34a90cf30c908f47f40ebea7811f743d360e202b6f10d40c02529ebd84afc069"}, @@ -3972,7 +3885,6 @@ description = "Protopunica is pomegranate frozen at version 0.14.8." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "protopunica-0.14.8.post2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:616313486a9c55e77c9ba0a3e05a7589216ed05b52908ffb95d4d74271f80f57"}, {file = "protopunica-0.14.8.post2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:07a0d5ce0037e0c89e021ec302ad8e9ee007fba93dde0f98a7d6fbd7d8849446"}, @@ -4011,7 +3923,6 @@ description = "Cross-platform lib for process and system monitoring in Python." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "psutil-6.1.0-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:ff34df86226c0227c52f38b919213157588a678d049688eded74c76c8ba4a5d0"}, {file = "psutil-6.1.0-cp27-cp27m-manylinux2010_i686.whl", hash = "sha256:c0e0c00aa18ca2d3b2b991643b799a15fc8f0563d2ebb6040f64ce8dc027b942"}, @@ -4043,7 +3954,7 @@ description = "Run a subprocess in a pseudo terminal" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" and os_name != \"nt\" or python_version <= \"3.11\" and (sys_platform != \"win32\" and sys_platform != \"emscripten\") or python_version >= \"3.12\" and extra == \"dev\" and os_name != \"nt\" or python_version >= \"3.12\" and (sys_platform != \"win32\" and sys_platform != \"emscripten\")" +markers = "extra == \"dev\" and os_name != \"nt\" or sys_platform != \"win32\" and sys_platform != \"emscripten\"" files = [ {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"}, {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"}, @@ -4056,7 +3967,6 @@ description = "Safely evaluate AST nodes without side effects" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pure_eval-0.2.3-py3-none-any.whl", hash = "sha256:1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0"}, {file = "pure_eval-0.2.3.tar.gz", hash = "sha256:5f4e983f40564c576c7c8635ae88db5956bb2229d7e9237d03b3c0b0190eaf42"}, @@ -4072,7 +3982,6 @@ description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pyasn1-0.6.1-py3-none-any.whl", hash = "sha256:0d632f46f2ba09143da3a8afe9e33fb6f92fa2320ab7e886e2d0f7672af84629"}, {file = "pyasn1-0.6.1.tar.gz", hash = "sha256:6f580d2bdd84365380830acf45550f2511469f673cb4a5ae3857a3170128b034"}, @@ -4085,7 +3994,6 @@ description = "A collection of ASN.1-based protocols modules" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pyasn1_modules-0.4.1-py3-none-any.whl", hash = "sha256:49bfa96b45a292b711e986f222502c1c9a5e1f4e568fc30e2574a6c7d07838fd"}, {file = "pyasn1_modules-0.4.1.tar.gz", hash = "sha256:c28e2dbf9c06ad61c71a075c7e0f9fd0f1b0bb2d2ad4377f240d33ac2ab60a7c"}, @@ -4101,7 +4009,7 @@ description = "C parser in Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and implementation_name == \"pypy\" or python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and implementation_name == \"pypy\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "implementation_name == \"pypy\" or extra == \"dev\"" files = [ {file = "pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc"}, {file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"}, @@ -4114,7 +4022,7 @@ description = "Bootstrap-based Sphinx theme from the PyData community" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pydata_sphinx_theme-0.16.0-py3-none-any.whl", hash = "sha256:18c810ee4e67e05281e371e156c1fb5bb0fa1f2747240461b225272f7d8d57d8"}, {file = "pydata_sphinx_theme-0.16.0.tar.gz", hash = "sha256:721dd26e05fa8b992d66ef545536e6cbe0110afb9865820a08894af1ad6f7707"}, @@ -4143,7 +4051,6 @@ description = "Pygments is a syntax highlighting package written in Python." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pygments-2.18.0-py3-none-any.whl", hash = "sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a"}, {file = "pygments-2.18.0.tar.gz", hash = "sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199"}, @@ -4159,7 +4066,7 @@ description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pytest-8.3.4-py3-none-any.whl", hash = "sha256:50e16d954148559c9a74109af1eaf0c945ba2d8f30f0a3d3335edde19788b6f6"}, {file = "pytest-8.3.4.tar.gz", hash = "sha256:965370d062bce11e73868e0335abac31b4d3de0e82f4007408d242b4f8610761"}, @@ -4183,7 +4090,7 @@ description = "Separate test code from test cases in pytest." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pytest_cases-3.8.6-py2.py3-none-any.whl", hash = "sha256:564c722492ea7e7ec3ac433fd14070180e65866f49fa35bfe938c0d5d9afba67"}, {file = "pytest_cases-3.8.6.tar.gz", hash = "sha256:5c24e0ab0cb6f8e802a469b7965906a333d3babb874586ebc56f7e2cbe1a7c44"}, @@ -4201,7 +4108,7 @@ description = "Pytest plugin for measuring coverage." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pytest-cov-6.0.0.tar.gz", hash = "sha256:fde0b595ca248bb8e2d76f020b465f3b107c9632e6a1d1705f17834c89dcadc0"}, {file = "pytest_cov-6.0.0-py3-none-any.whl", hash = "sha256:eee6f1b9e61008bd34975a4d5bab25801eb31898b032dd55addc93e96fcaaa35"}, @@ -4221,7 +4128,7 @@ description = "pytest xdist plugin for distributed testing, most importantly acr optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pytest_xdist-3.6.1-py3-none-any.whl", hash = "sha256:9ed4adfb68a016610848639bb7e02c9352d5d9f03d04809919e2dafc3be4cca7"}, {file = "pytest_xdist-3.6.1.tar.gz", hash = "sha256:ead156a4db231eec769737f57668ef58a2084a34b2e55c4a8fa20d861107300d"}, @@ -4243,7 +4150,6 @@ description = "Extensions to the standard Python datetime module" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"}, {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"}, @@ -4259,7 +4165,7 @@ description = "A python library adding a json log formatter" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "python-json-logger-2.0.7.tar.gz", hash = "sha256:23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c"}, {file = "python_json_logger-2.0.7-py3-none-any.whl", hash = "sha256:f380b826a991ebbe3de4d897aeec42760035ac760345e57b812938dc8b35e2bd"}, @@ -4272,7 +4178,6 @@ description = "World timezone definitions, modern and historical" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pytz-2024.2-py2.py3-none-any.whl", hash = "sha256:31c7c1817eb7fae7ca4b8c7ee50c72f93aa2dd863de768e1ef4245d426aa0725"}, {file = "pytz-2024.2.tar.gz", hash = "sha256:2aa355083c50a0f93fa581709deac0c9ad65cca8a9e9beac660adcbd493c798a"}, @@ -4285,7 +4190,7 @@ description = "Python for Window Extensions" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and sys_platform == \"win32\" and platform_python_implementation != \"PyPy\" or python_version >= \"3.12\" and sys_platform == \"win32\" and platform_python_implementation != \"PyPy\"" +markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\"" files = [ {file = "pywin32-308-cp310-cp310-win32.whl", hash = "sha256:796ff4426437896550d2981b9c2ac0ffd75238ad9ea2d3bfa67a1abd546d262e"}, {file = "pywin32-308-cp310-cp310-win_amd64.whl", hash = "sha256:4fc888c59b3c0bef905ce7eb7e2106a07712015ea1c8234b703a088d46110e8e"}, @@ -4314,7 +4219,7 @@ description = "Pseudo terminal support for Windows from Python." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" and os_name == \"nt\" or python_version >= \"3.12\" and extra == \"dev\" and os_name == \"nt\"" +markers = "extra == \"dev\" and os_name == \"nt\"" files = [ {file = "pywinpty-2.0.14-cp310-none-win_amd64.whl", hash = "sha256:0b149c2918c7974f575ba79f5a4aad58bd859a52fa9eb1296cc22aa412aa411f"}, {file = "pywinpty-2.0.14-cp311-none-win_amd64.whl", hash = "sha256:cf2a43ac7065b3e0dc8510f8c1f13a75fb8fde805efa3b8cff7599a1ef497bc7"}, @@ -4331,7 +4236,6 @@ description = "YAML parser and emitter for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0a9a2848a5b7feac301353437eb7d5957887edbf81d56e903999a75a3d743086"}, {file = "PyYAML-6.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:29717114e51c84ddfba879543fb232a6ed60086602313ca38cce623c1d62cfbf"}, @@ -4395,7 +4299,6 @@ description = "Python bindings for 0MQ" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pyzmq-26.2.0-cp310-cp310-macosx_10_15_universal2.whl", hash = "sha256:ddf33d97d2f52d89f6e6e7ae66ee35a4d9ca6f36eda89c24591b0c40205a3629"}, {file = "pyzmq-26.2.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dacd995031a01d16eec825bf30802fceb2c3791ef24bcce48fa98ce40918c27b"}, @@ -4518,7 +4421,7 @@ description = "JSON Referencing + Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "referencing-0.35.1-py3-none-any.whl", hash = "sha256:eda6d3234d62814d1c64e305c1331c9a3a6132da475ab6382eaa997b21ee75de"}, {file = "referencing-0.35.1.tar.gz", hash = "sha256:25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c"}, @@ -4535,7 +4438,6 @@ description = "Python HTTP for Humans." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"}, {file = "requests-2.32.3.tar.gz", hash = "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"}, @@ -4558,7 +4460,6 @@ description = "OAuthlib authentication support for Requests." optional = false python-versions = ">=3.4" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "requests-oauthlib-2.0.0.tar.gz", hash = "sha256:b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9"}, {file = "requests_oauthlib-2.0.0-py2.py3-none-any.whl", hash = "sha256:7dd8a5c40426b779b0868c404bdef9768deccf22749cde15852df527e6269b36"}, @@ -4578,7 +4479,6 @@ description = "Retrying" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "retrying-1.3.4-py3-none-any.whl", hash = "sha256:8cc4d43cb8e1125e0ff3344e9de678fefd85db3b750b81b2240dc0183af37b35"}, {file = "retrying-1.3.4.tar.gz", hash = "sha256:345da8c5765bd982b1d1915deb9102fd3d1f7ad16bd84a9700b85f64d24e8f3e"}, @@ -4594,7 +4494,7 @@ description = "A pure python RFC3339 validator" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "rfc3339_validator-0.1.4-py2.py3-none-any.whl", hash = "sha256:24f6ec1eda14ef823da9e36ec7113124b39c04d50a4d3d3a3c2859577e7791fa"}, {file = "rfc3339_validator-0.1.4.tar.gz", hash = "sha256:138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b"}, @@ -4610,7 +4510,7 @@ description = "Pure python rfc3986 validator" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "rfc3986_validator-0.1.1-py2.py3-none-any.whl", hash = "sha256:2f235c432ef459970b4306369336b9d5dbdda31b510ca1e327636e01f528bfa9"}, {file = "rfc3986_validator-0.1.1.tar.gz", hash = "sha256:3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055"}, @@ -4623,7 +4523,7 @@ description = "Python bindings to Rust's persistent data structures (rpds)" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "rpds_py-0.22.3-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:6c7b99ca52c2c1752b544e310101b98a659b720b21db00e65edca34483259967"}, {file = "rpds_py-0.22.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:be2eb3f2495ba669d2a985f9b426c1797b7d48d6963899276d22f23e33d47e37"}, @@ -4737,7 +4637,6 @@ description = "Pure-Python RSA implementation" optional = false python-versions = ">=3.6,<4" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "rsa-4.9-py3-none-any.whl", hash = "sha256:90260d9058e514786967344d0ef75fa8727eed8a7d2e43ce9f4bcf1b536174f7"}, {file = "rsa-4.9.tar.gz", hash = "sha256:e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21"}, @@ -4753,7 +4652,7 @@ description = "An extremely fast Python linter and code formatter, written in Ru optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "ruff-0.8.1-py3-none-linux_armv6l.whl", hash = "sha256:fae0805bd514066f20309f6742f6ee7904a773eb9e6c17c45d6b1600ca65c9b5"}, {file = "ruff-0.8.1-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:b8a4f7385c2285c30f34b200ca5511fcc865f17578383db154e098150ce0a087"}, @@ -4782,7 +4681,6 @@ description = "Convenient Filesystem interface over S3" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "s3fs-2024.10.0-py3-none-any.whl", hash = "sha256:7a2025d60d5b1a6025726b3a5e292a8e5aa713abc3b16fd1f81735181f7bb282"}, {file = "s3fs-2024.10.0.tar.gz", hash = "sha256:58b8c3650f8b99dbedf361543da3533aac8707035a104db5d80b094617ad4a3f"}, @@ -4804,7 +4702,6 @@ description = "A Python package for exploring and analysing genetic variation da optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "scikit_allel-1.3.13-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:eb786c909c34b682205c3cacba9b4f0866e658917f30e2f97e1051d9fb2e7ccc"}, {file = "scikit_allel-1.3.13-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1853068621208fc2d5537e9a5b292aef2d5e8c975fa35f8f810b3174e0226160"}, @@ -4839,7 +4736,6 @@ description = "Fundamental algorithms for scientific computing in Python" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "scipy-1.14.1-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:b28d2ca4add7ac16ae8bb6632a3c86e4b9e4d52d3e34267f6e1b0c1f8d87e389"}, {file = "scipy-1.14.1-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:d0d2821003174de06b69e58cef2316a6622b60ee613121199cb2852a873f8cf3"}, @@ -4882,7 +4778,7 @@ numpy = ">=1.23.5,<2.3" [package.extras] dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"] doc = ["jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.13.1)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<=7.3.7)", "sphinx-design (>=0.4.0)"] -test = ["Cython", "array-api-strict (>=2.0)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] +test = ["Cython", "array-api-strict (>=2.0)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] [[package]] name = "send2trash" @@ -4891,16 +4787,16 @@ description = "Send file to trash natively under Mac OS X, Windows and Linux" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "Send2Trash-1.8.3-py3-none-any.whl", hash = "sha256:0c31227e0bd08961c7665474a3d1ef7193929fedda4233843689baa056be46c9"}, {file = "Send2Trash-1.8.3.tar.gz", hash = "sha256:b18e7a3966d99871aefeb00cfbcfdced55ce4871194810fc71f4aa484b953abf"}, ] [package.extras] -nativelib = ["pyobjc-framework-Cocoa", "pywin32"] -objc = ["pyobjc-framework-Cocoa"] -win32 = ["pywin32"] +nativelib = ["pyobjc-framework-Cocoa ; sys_platform == \"darwin\"", "pywin32 ; sys_platform == \"win32\""] +objc = ["pyobjc-framework-Cocoa ; sys_platform == \"darwin\""] +win32 = ["pywin32 ; sys_platform == \"win32\""] [[package]] name = "setuptools" @@ -4909,20 +4805,19 @@ description = "Easily download, build, install, upgrade, and uninstall Python pa optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "setuptools-75.6.0-py3-none-any.whl", hash = "sha256:ce74b49e8f7110f9bf04883b730f4765b774ef3ef28f722cce7c273d253aaf7d"}, {file = "setuptools-75.6.0.tar.gz", hash = "sha256:8199222558df7c86216af4f84c30e9b34a61d8ba19366cc914424cdbd28252f6"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.7.0)"] -core = ["importlib_metadata (>=6)", "jaraco.collections", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\"", "ruff (>=0.7.0) ; sys_platform != \"cygwin\""] +core = ["importlib_metadata (>=6) ; python_version < \"3.10\"", "jaraco.collections", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1) ; python_version < \"3.11\"", "wheel (>=0.43.0)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"] enabler = ["pytest-enabler (>=2.2)"] -test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] -type = ["importlib_metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (>=1.12,<1.14)", "pytest-mypy"] +test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21) ; python_version >= \"3.9\" and sys_platform != \"cygwin\"", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf ; sys_platform != \"cygwin\"", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] +type = ["importlib_metadata (>=7.0.2) ; python_version < \"3.10\"", "jaraco.develop (>=7.21) ; sys_platform != \"cygwin\"", "mypy (>=1.12,<1.14)", "pytest-mypy"] [[package]] name = "six" @@ -4931,7 +4826,6 @@ description = "Python 2 and 3 compatibility utilities" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"}, {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, @@ -4944,7 +4838,7 @@ description = "A web-based viewer for Python profiler output" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "snakeviz-2.2.2-py3-none-any.whl", hash = "sha256:77e7b9c82f6152edc330040319b97612351cd9b48c706434c535c2df31d10ac5"}, {file = "snakeviz-2.2.2.tar.gz", hash = "sha256:08028c6f8e34a032ff14757a38424770abb8662fb2818985aeea0d9bc13a7d83"}, @@ -4960,7 +4854,7 @@ description = "Sniff out which async library your code is running under" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2"}, {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"}, @@ -4973,7 +4867,7 @@ description = "This package provides 29 stemmers for 28 languages generated from optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"}, {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"}, @@ -4986,7 +4880,6 @@ description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0"}, {file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"}, @@ -4999,7 +4892,7 @@ description = "A modern CSS selector implementation for Beautiful Soup." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "soupsieve-2.6-py3-none-any.whl", hash = "sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9"}, {file = "soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb"}, @@ -5012,7 +4905,7 @@ description = "Python documentation generator" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinx-8.1.3-py3-none-any.whl", hash = "sha256:09719015511837b76bf6e03e42eb7595ac8c2e41eeb9c29c5b755c6b677992a2"}, {file = "sphinx-8.1.3.tar.gz", hash = "sha256:43c1911eecb0d3e161ad78611bc905d1ad0e523e4ddc202a58a821773dc4c927"}, @@ -5049,7 +4942,7 @@ description = "A sphinx extension for designing beautiful, view size responsive optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinx_design-0.6.1-py3-none-any.whl", hash = "sha256:b11f37db1a802a183d61b159d9a202314d4d2fe29c163437001324fe2f19549c"}, {file = "sphinx_design-0.6.1.tar.gz", hash = "sha256:b44eea3719386d04d765c1a8257caca2b3e6f8421d7b3a5e742c0fd45f84e632"}, @@ -5076,7 +4969,7 @@ description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"}, {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"}, @@ -5094,7 +4987,7 @@ description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"}, {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"}, @@ -5112,7 +5005,7 @@ description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML h optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"}, {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"}, @@ -5130,7 +5023,7 @@ description = "A sphinx extension which renders display math in HTML via JavaScr optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"}, {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"}, @@ -5146,7 +5039,7 @@ description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp d optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"}, {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"}, @@ -5164,7 +5057,7 @@ description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"}, {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"}, @@ -5182,7 +5075,6 @@ description = "Extract data from python stack frames and tracebacks for informat optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"}, {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"}, @@ -5203,7 +5095,6 @@ description = "Statistical computations and models for Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "statsmodels-0.14.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:7a62f1fc9086e4b7ee789a6f66b3c0fc82dd8de1edda1522d30901a0aa45e42b"}, {file = "statsmodels-0.14.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:46ac7ddefac0c9b7b607eed1d47d11e26fe92a1bc1f4d9af48aeed4e21e87981"}, @@ -5246,7 +5137,7 @@ scipy = ">=1.8,<1.9.2 || >1.9.2" [package.extras] build = ["cython (>=3.0.10)"] -develop = ["colorama", "cython (>=3.0.10)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools-scm[toml] (>=8.0,<9.0)"] +develop = ["colorama", "cython (>=3.0.10)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty ; os_name == \"nt\"", "setuptools-scm[toml] (>=8.0,<9.0)"] docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"] [[package]] @@ -5256,7 +5147,6 @@ description = "Traceback serialization library." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tblib-3.0.0-py3-none-any.whl", hash = "sha256:80a6c77e59b55e83911e1e607c649836a69c103963c5f28a46cbeef44acf8129"}, {file = "tblib-3.0.0.tar.gz", hash = "sha256:93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6"}, @@ -5269,7 +5159,6 @@ description = "Retry code until it succeeds" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tenacity-9.0.0-py3-none-any.whl", hash = "sha256:93de0c98785b27fcf659856aa9f54bfbd399e29969b0621bc7f762bd441b4539"}, {file = "tenacity-9.0.0.tar.gz", hash = "sha256:807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b"}, @@ -5286,7 +5175,6 @@ description = "ANSI color formatting for output in terminal" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "termcolor-2.3.0-py3-none-any.whl", hash = "sha256:3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475"}, {file = "termcolor-2.3.0.tar.gz", hash = "sha256:b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a"}, @@ -5302,7 +5190,7 @@ description = "Tornado websocket backend for the Xterm.js Javascript terminal em optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "terminado-0.18.1-py3-none-any.whl", hash = "sha256:a4468e1b37bb318f8a86514f65814e1afc977cf29b3992a4500d9dd305dcceb0"}, {file = "terminado-0.18.1.tar.gz", hash = "sha256:de09f2c4b85de4765f7714688fff57d3e75bad1f909b589fde880460c753fd2e"}, @@ -5325,7 +5213,7 @@ description = "A tiny CSS parser" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "tinycss2-1.4.0-py3-none-any.whl", hash = "sha256:3a49cf47b7675da0b15d0c6e1df8df4ebd96e9394bb905a5775adb0d884c5289"}, {file = "tinycss2-1.4.0.tar.gz", hash = "sha256:10c0972f6fc0fbee87c3edb76549357415e94548c1ae10ebccdea16fb404a9b7"}, @@ -5345,7 +5233,7 @@ description = "A lil' TOML parser" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_full_version <= \"3.11.0a6\" and extra == \"dev\"" +markers = "extra == \"dev\" and python_version == \"3.10\"" files = [ {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"}, {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"}, @@ -5388,7 +5276,6 @@ description = "List processing tools and functional utilities" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "toolz-1.0.0-py3-none-any.whl", hash = "sha256:292c8f1c4e7516bf9086f8850935c799a874039c8bcf959d47b600e4c44a6236"}, {file = "toolz-1.0.0.tar.gz", hash = "sha256:2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02"}, @@ -5401,7 +5288,6 @@ description = "Tornado is a Python web framework and asynchronous networking lib optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:e828cce1123e9e44ae2a50a9de3055497ab1d0aeb440c5ac23064d9e44880da1"}, {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_x86_64.whl", hash = "sha256:072ce12ada169c5b00b7d92a99ba089447ccc993ea2143c9ede887e0937aa803"}, @@ -5423,7 +5309,6 @@ description = "Fast, Extensible Progress Meter" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2"}, {file = "tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2"}, @@ -5446,7 +5331,6 @@ description = "Traitlets Python configuration system" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"}, {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"}, @@ -5463,7 +5347,6 @@ description = "Scipy trait types" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "traittypes-0.2.1-py2.py3-none-any.whl", hash = "sha256:1340af133810b6eee1a2eb2e988f862b0d12b6c2d16f282aaf3207b782134c2e"}, {file = "traittypes-0.2.1.tar.gz", hash = "sha256:be6fa26294733e7489822ded4ae25da5b4824a8a7a0e0c2dccfde596e3489bd6"}, @@ -5482,7 +5365,6 @@ description = "Run-time type checker for Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "typeguard-4.4.1-py3-none-any.whl", hash = "sha256:9324ec07a27ec67fc54a9c063020ca4c0ae6abad5e9f0f9804ca59aee68c6e21"}, {file = "typeguard-4.4.1.tar.gz", hash = "sha256:0d22a89d00b453b47c49875f42b6601b961757541a2e1e0ef517b6e24213c21b"}, @@ -5493,7 +5375,7 @@ typing-extensions = ">=4.10.0" [package.extras] doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.3.0)"] -test = ["coverage[toml] (>=7)", "mypy (>=1.2.0)", "pytest (>=7)"] +test = ["coverage[toml] (>=7)", "mypy (>=1.2.0) ; platform_python_implementation != \"PyPy\"", "pytest (>=7)"] [[package]] name = "types-python-dateutil" @@ -5502,7 +5384,7 @@ description = "Typing stubs for python-dateutil" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "types-python-dateutil-2.9.0.20241003.tar.gz", hash = "sha256:58cb85449b2a56d6684e41aeefb4c4280631246a0da1a719bdbe6f3fb0317446"}, {file = "types_python_dateutil-2.9.0.20241003-py3-none-any.whl", hash = "sha256:250e1d8e80e7bbc3a6c99b907762711d1a1cdd00e978ad39cb5940f6f0a87f3d"}, @@ -5515,7 +5397,7 @@ description = "Typing stubs for pytz" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "types-pytz-2024.2.0.20241003.tar.gz", hash = "sha256:575dc38f385a922a212bac00a7d6d2e16e141132a3c955078f4a4fd13ed6cb44"}, {file = "types_pytz-2024.2.0.20241003-py3-none-any.whl", hash = "sha256:3e22df1336c0c6ad1d29163c8fda82736909eb977281cb823c57f8bae07118b7"}, @@ -5528,7 +5410,6 @@ description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, @@ -5541,7 +5422,6 @@ description = "Provider of IANA time zone data" optional = false python-versions = ">=2" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"}, {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"}, @@ -5554,7 +5434,7 @@ description = "RFC 6570 URI Template Processor" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "uri-template-1.3.0.tar.gz", hash = "sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7"}, {file = "uri_template-1.3.0-py3-none-any.whl", hash = "sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363"}, @@ -5570,14 +5450,13 @@ description = "HTTP library with thread-safe connection pooling, file post, and optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"}, {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"}, ] [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""] h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] @@ -5589,7 +5468,7 @@ description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "virtualenv-20.28.0-py3-none-any.whl", hash = "sha256:23eae1b4516ecd610481eda647f3a7c09aea295055337331bb4e6892ecce47b0"}, {file = "virtualenv-20.28.0.tar.gz", hash = "sha256:2c9c3262bb8e7b87ea801d715fae4495e6032450c71d2309be9550e7364049aa"}, @@ -5602,7 +5481,7 @@ platformdirs = ">=3.9.1,<5" [package.extras] docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""] [[package]] name = "wcwidth" @@ -5611,7 +5490,6 @@ description = "Measures the displayed width of unicode strings in a terminal" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, @@ -5624,7 +5502,7 @@ description = "A library for working with the color formats defined by HTML and optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "webcolors-24.11.1-py3-none-any.whl", hash = "sha256:515291393b4cdf0eb19c155749a096f779f7d909f7cceea072791cb9095b92e9"}, {file = "webcolors-24.11.1.tar.gz", hash = "sha256:ecb3d768f32202af770477b8b65f318fa4f566c22948673a977b00d589dd80f6"}, @@ -5637,7 +5515,7 @@ description = "Character encoding aliases for legacy web content" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, @@ -5650,7 +5528,7 @@ description = "WebSocket client for Python with low level API options" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"}, {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"}, @@ -5668,7 +5546,6 @@ description = "The comprehensive WSGI web application library." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "werkzeug-3.0.6-py3-none-any.whl", hash = "sha256:1bc0c2310d2fbb07b1dd1105eba2f7af72f322e1e455f2f93c993bee8c8a5f17"}, {file = "werkzeug-3.0.6.tar.gz", hash = "sha256:a8dd59d4de28ca70471a34cba79bed5f7ef2e036a76b3ab0835474246eb41f8d"}, @@ -5687,7 +5564,6 @@ description = "Jupyter interactive widgets for Jupyter Notebook" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71"}, {file = "widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6"}, @@ -5700,7 +5576,6 @@ description = "Module for decorators, wrappers and monkey patching." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "wrapt-1.17.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2a0c23b8319848426f305f9cb0c98a6e32ee68a36264f45948ccf8e7d2b941f8"}, {file = "wrapt-1.17.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b1ca5f060e205f72bec57faae5bd817a1560fcfc4af03f414b08fa29106b7e2d"}, @@ -5776,7 +5651,6 @@ description = "N-D labeled arrays and datasets in Python" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "xarray-2024.11.0-py3-none-any.whl", hash = "sha256:6ee94f63ddcbdd0cf3909d1177f78cdac756640279c0e32ae36819a89cdaba37"}, {file = "xarray-2024.11.0.tar.gz", hash = "sha256:1ccace44573ddb862e210ad3ec204210654d2c750bec11bbe7d842dfc298591f"}, @@ -5792,7 +5666,7 @@ accel = ["bottleneck", "flox", "numba (>=0.54)", "numbagg", "opt_einsum", "scipy complete = ["xarray[accel,etc,io,parallel,viz]"] dev = ["hypothesis", "jinja2", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "ruff", "sphinx", "sphinx_autosummary_accessors", "xarray[complete]"] etc = ["sparse"] -io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"] +io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap ; python_version < \"3.10\"", "scipy", "zarr"] parallel = ["dask[complete]"] viz = ["cartopy", "matplotlib", "nc-time-axis", "seaborn"] @@ -5803,7 +5677,6 @@ description = "Source of XYZ tiles providers" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "xyzservices-2024.9.0-py3-none-any.whl", hash = "sha256:776ae82b78d6e5ca63dd6a94abb054df8130887a4a308473b54a6bd364de8644"}, {file = "xyzservices-2024.9.0.tar.gz", hash = "sha256:68fb8353c9dbba4f1ff6c0f2e5e4e596bb9e1db7f94f4f7dfbcb26e25aa66fde"}, @@ -5816,7 +5689,6 @@ description = "Yet another URL library" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7df647e8edd71f000a5208fe6ff8c382a1de8edfbccdbbfe649d263de07d8c34"}, {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c69697d3adff5aa4f874b19c0e4ed65180ceed6318ec856ebc423aa5850d84f7"}, @@ -5914,7 +5786,6 @@ description = "Yet Another Terminal Spinner" optional = false python-versions = "<4.0,>=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "yaspin-3.1.0-py3-none-any.whl", hash = "sha256:5e3d4dfb547d942cae6565718123f1ecfa93e745b7e51871ad2bbae839e71b73"}, {file = "yaspin-3.1.0.tar.gz", hash = "sha256:7b97c7e257ec598f98cef9878e038bfa619ceb54ac31d61d8ead2b3128f8d7c7"}, @@ -5930,7 +5801,6 @@ description = "An implementation of chunked, compressed, N-dimensional arrays fo optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "zarr-2.18.3-py3-none-any.whl", hash = "sha256:b1f7dfd2496f436745cdd4c7bcf8d3b4bc1dceef5fdd0d589c87130d842496dd"}, {file = "zarr-2.18.3.tar.gz", hash = "sha256:2580d8cb6dd84621771a10d31c4d777dca8a27706a1a89b29f42d2d37e2df5ce"}, @@ -5953,7 +5823,6 @@ description = "Mutable mapping tools" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "zict-3.0.0-py2.py3-none-any.whl", hash = "sha256:5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae"}, {file = "zict-3.0.0.tar.gz", hash = "sha256:e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5"}, @@ -5966,18 +5835,17 @@ description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"}, {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] [extras] @@ -5986,4 +5854,4 @@ dev = ["jupyterlab", "memory-profiler", "mypy", "notebook", "pandas-stubs", "pre [metadata] lock-version = "2.1" python-versions = ">=3.10,<3.13" -content-hash = "d6919913d2daade4ac3ff27f8813d3286edb5129809eda93f2fc9cb3c032cd88" +content-hash = "e2dc0c54942b1e2261de9c28a0c3750350ff2bb6aa20700a71ec8fba81e1382a" diff --git a/pyproject.toml b/pyproject.toml index af428de94..f6d2cd953 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -84,6 +84,7 @@ sphinx = "*" pydata-sphinx-theme = "*" sphinx_design = "*" pandas-stubs = "*" +ipykernel = "^6.29.5" [tool.poetry.extras] dev = ["pytest", "pytest-xdist", "pytest-cases", "pytest-cov", "notebook", "jupyterlab", "pre-commit", "ruff", "snakeviz", "mypy", "memory-profiler", "sphinx", "pydata-sphinx-theme", "sphinx_design", "pandas-stubs"] From 15c9b2869c87b75b0c877d05cb59c77f41eabb7f Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Mon, 9 Jun 2025 14:45:18 +1000 Subject: [PATCH 07/41] add adir1 class for anopheles dirus data release --- adir1_explore.ipynb | 451 ++++++++++++++++++++++++++++++++++++ malariagen_data/__init__.py | 1 + malariagen_data/adir1.py | 208 +++++++++++++++++ 3 files changed, 660 insertions(+) create mode 100644 adir1_explore.ipynb create mode 100644 malariagen_data/adir1.py diff --git a/adir1_explore.ipynb b/adir1_explore.ipynb new file mode 100644 index 000000000..c42d93dd5 --- /dev/null +++ b/adir1_explore.ipynb @@ -0,0 +1,451 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import malariagen_data" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "'use strict';\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " const force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + "const JS_MIME_TYPE = 'application/javascript';\n", + " const HTML_MIME_TYPE = 'text/html';\n", + " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " const CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " const script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\n", + " const cell = handle.cell;\n", + "\n", + " const id = cell.output_area._bokeh_element_id;\n", + " const server_id = cell.output_area._bokeh_server_id;\n", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(id)\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd_clean, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " const id = msg.content.text.trim()\n", + " drop(id)\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd_destroy);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " const output_area = handle.output_area;\n", + " const output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " const bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " const script_attrs = bk_div.children[0].attributes;\n", + " for (let i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " const toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"
    \\n\"+\n", + " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", + " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", + " \"
\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded(error = null) {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " const html = (() => {\n", + " if (typeof root.Bokeh === \"undefined\") {\n", + " if (error == null) {\n", + " return \"BokehJS is loading ...\";\n", + " } else {\n", + " return \"BokehJS failed to load.\";\n", + " }\n", + " } else {\n", + " const prefix = `BokehJS ${root.Bokeh.version}`;\n", + " if (error == null) {\n", + " return `${prefix} successfully loaded.`;\n", + " } else {\n", + " return `${prefix} encountered errors while loading and may not function as expected.`;\n", + " }\n", + " }\n", + " })();\n", + " el.innerHTML = html;\n", + "\n", + " if (error != null) {\n", + " const wrapper = document.createElement(\"div\");\n", + " wrapper.style.overflow = \"auto\";\n", + " wrapper.style.height = \"5em\";\n", + " wrapper.style.resize = \"vertical\";\n", + " const content = document.createElement(\"div\");\n", + " content.style.fontFamily = \"monospace\";\n", + " content.style.whiteSpace = \"pre-wrap\";\n", + " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", + " content.textContent = error.stack ?? error.toString();\n", + " wrapper.append(content);\n", + " el.append(wrapper);\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(() => display_loaded(error), 100);\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " try {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "\n", + " } catch (error) {throw error;\n", + " }} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Init API\n", + "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "f171c3b7-30c2-4e9f-9133-22206985de07", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'KB672868'" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Are the contigs here? \n", + "chroms = adir1.contigs[:5]\n", + "chroms[1]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "ename": "FileNotFoundError", + "evalue": "b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:426\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 425\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_sets\u001b[49m\u001b[43m[\u001b[49m\u001b[43mrelease\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n", + "\u001b[0;31mKeyError\u001b[0m: '1.x'", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m snps \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msnp_calls\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868:1000000-2000000\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/snp_data.py:1007\u001b[0m, in \u001b[0;36mAnophelesSnpData.snp_calls\u001b[0;34m(self, region, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, inline_array, chunks, cohort_size, min_cohort_size, max_cohort_size, random_seed)\u001b[0m\n\u001b[1;32m 1001\u001b[0m base_params\u001b[38;5;241m.\u001b[39mvalidate_sample_selection_params(\n\u001b[1;32m 1002\u001b[0m sample_query\u001b[38;5;241m=\u001b[39msample_query, sample_indices\u001b[38;5;241m=\u001b[39msample_indices\n\u001b[1;32m 1003\u001b[0m )\n\u001b[1;32m 1005\u001b[0m \u001b[38;5;66;03m# Normalise parameters.\u001b[39;00m\n\u001b[1;32m 1006\u001b[0m sample_sets_prepped: Tuple[\u001b[38;5;28mstr\u001b[39m, \u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mtuple\u001b[39m(\n\u001b[0;32m-> 1007\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_sets_param\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1008\u001b[0m )\n\u001b[1;32m 1009\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m sample_sets\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_indices \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:524\u001b[0m, in \u001b[0;36mAnophelesBase._prep_sample_sets_param\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_prep_sample_sets_param\u001b[39m(\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets]\n\u001b[1;32m 519\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m List[\u001b[38;5;28mstr\u001b[39m]:\n\u001b[1;32m 520\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Common handling for the `sample_sets` parameter. For convenience, we\u001b[39;00m\n\u001b[1;32m 521\u001b[0m \u001b[38;5;124;03m allow this to be a single sample set, or a list of sample sets, or a\u001b[39;00m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;124;03m release identifier, or a list of release identifiers.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 524\u001b[0m all_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_list()\n\u001b[1;32m 526\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_sets \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 527\u001b[0m \u001b[38;5;66;03m# All available sample sets.\u001b[39;00m\n\u001b[1;32m 528\u001b[0m prepped_sample_sets \u001b[38;5;241m=\u001b[39m all_sample_sets\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets(release\u001b[38;5;241m=\u001b[39mr) \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrelease\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mr\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:430\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release]\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n\u001b[0;32m--> 430\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_sample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43msingle_release\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrelease\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 431\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release] \u001b[38;5;241m=\u001b[39m df\n\u001b[1;32m 433\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(release, Sequence):\n\u001b[1;32m 434\u001b[0m \u001b[38;5;66;03m# Ensure no duplicates.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:376\u001b[0m, in \u001b[0;36mAnophelesBase._read_sample_sets\u001b[0;34m(self, single_release)\u001b[0m\n\u001b[1;32m 373\u001b[0m manifest_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrelease_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/manifest.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 375\u001b[0m \u001b[38;5;66;03m# Read the manifest into a pandas dataframe.\u001b[39;00m\n\u001b[0;32m--> 376\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmanifest_path\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 377\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mread_csv(f, sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, na_values\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 379\u001b[0m \u001b[38;5;66;03m# Add a \"release\" column for convenience.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:218\u001b[0m, in \u001b[0;36mAnophelesBase.open_file\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_file\u001b[39m(\u001b[38;5;28mself\u001b[39m, path: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m IO:\n\u001b[1;32m 217\u001b[0m full_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_base_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 218\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfull_path\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1154\u001b[0m, in \u001b[0;36mAbstractFileSystem.open\u001b[0;34m(self, path, mode, block_size, cache_options, compression, **kwargs)\u001b[0m\n\u001b[1;32m 1152\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1153\u001b[0m ac \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mautocommit\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_intrans)\n\u001b[0;32m-> 1154\u001b[0m f \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_open\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1155\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1156\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1157\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1158\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mac\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1159\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1161\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfsspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcompression\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m compr\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1309\u001b[0m, in \u001b[0;36mGCSFileSystem._open\u001b[0;34m(self, path, mode, block_size, cache_options, acl, consistency, metadata, autocommit, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1307\u001b[0m block_size \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_block_size\n\u001b[1;32m 1308\u001b[0m const \u001b[38;5;241m=\u001b[39m consistency \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconsistency\n\u001b[0;32m-> 1309\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mGCSFile\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1311\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1312\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1313\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1314\u001b[0m \u001b[43m 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\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1321\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1468\u001b[0m, in \u001b[0;36mGCSFile.__init__\u001b[0;34m(self, gcsfs, path, mode, block_size, autocommit, cache_type, cache_options, acl, consistency, metadata, content_type, timeout, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1466\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAttempt to open a bucket\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1467\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgeneration \u001b[38;5;241m=\u001b[39m _coalesce_generation(generation, path_generation)\n\u001b[0;32m-> 1468\u001b[0m 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1509\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1510\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdetails\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msize\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m 1511\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcache \u001b[38;5;241m=\u001b[39m caches[cache_type](\n\u001b[1;32m 1512\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mblocksize, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fetch_range, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mcache_options\n\u001b[1;32m 1513\u001b[0m )\n\u001b[1;32m 1514\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1504\u001b[0m, in \u001b[0;36mGCSFile.details\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1501\u001b[0m \u001b[38;5;129m@property\u001b[39m\n\u001b[1;32m 1502\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdetails\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[1;32m 1503\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 1504\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minfo\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m 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\u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloop\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:100\u001b[0m, in \u001b[0;36msync\u001b[0;34m(loop, func, timeout, *args, **kwargs)\u001b[0m\n\u001b[1;32m 98\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m FSTimeoutError \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mreturn_result\u001b[39;00m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(return_result, \u001b[38;5;167;01mBaseException\u001b[39;00m):\n\u001b[0;32m--> 100\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m return_result\n\u001b[1;32m 101\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 102\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m return_result\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:55\u001b[0m, in \u001b[0;36m_runner\u001b[0;34m(event, coro, result, timeout)\u001b[0m\n\u001b[1;32m 53\u001b[0m coro \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mwait_for(coro, timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m 54\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 55\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 56\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m ex:\n\u001b[1;32m 57\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m ex\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:797\u001b[0m, in \u001b[0;36mGCSFileSystem._info\u001b[0;34m(self, path, generation, **kwargs)\u001b[0m\n\u001b[1;32m 795\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 796\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdetail\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m \u001b[38;5;66;03m# Force to true for info\u001b[39;00m\n\u001b[0;32m--> 797\u001b[0m out \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ls(path, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 798\u001b[0m out0 \u001b[38;5;241m=\u001b[39m [o \u001b[38;5;28;01mfor\u001b[39;00m o \u001b[38;5;129;01min\u001b[39;00m out \u001b[38;5;28;01mif\u001b[39;00m o[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mrstrip(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m==\u001b[39m path]\n\u001b[1;32m 799\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m out0:\n\u001b[1;32m 800\u001b[0m \u001b[38;5;66;03m# exact hit\u001b[39;00m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:834\u001b[0m, in \u001b[0;36mGCSFileSystem._ls\u001b[0;34m(self, path, detail, prefix, versions, **kwargs)\u001b[0m\n\u001b[1;32m 832\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 833\u001b[0m out \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 834\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m entry \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_list_objects(\n\u001b[1;32m 835\u001b[0m path, prefix\u001b[38;5;241m=\u001b[39mprefix, versions\u001b[38;5;241m=\u001b[39mversions\n\u001b[1;32m 836\u001b[0m ):\n\u001b[1;32m 837\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m versions \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeneration\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m entry:\n\u001b[1;32m 838\u001b[0m entry \u001b[38;5;241m=\u001b[39m entry\u001b[38;5;241m.\u001b[39mcopy()\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:549\u001b[0m, in \u001b[0;36mGCSFileSystem._list_objects\u001b[0;34m(self, path, prefix, versions)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (items \u001b[38;5;241m+\u001b[39m pseudodirs):\n\u001b[1;32m 548\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m key:\n\u001b[0;32m--> 549\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_object(path)]\n\u001b[1;32m 550\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 551\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m []\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:491\u001b[0m, in \u001b[0;36mGCSFileSystem._get_object\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 488\u001b[0m \u001b[38;5;66;03m# Work around various permission settings. Prefer an object get (storage.objects.get), but\u001b[39;00m\n\u001b[1;32m 489\u001b[0m \u001b[38;5;66;03m# fall back to a bucket list + filter to object name (storage.objects.list).\u001b[39;00m\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 491\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_call(\n\u001b[1;32m 492\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGET\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/o/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, bucket, key, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, generation\u001b[38;5;241m=\u001b[39mgeneration\n\u001b[1;32m 493\u001b[0m )\n\u001b[1;32m 494\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 495\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(e)\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mForbidden\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:418\u001b[0m, in \u001b[0;36mGCSFileSystem._call\u001b[0;34m(self, method, path, json_out, info_out, *args, **kwargs)\u001b[0m\n\u001b[1;32m 414\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_call\u001b[39m(\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28mself\u001b[39m, method, path, \u001b[38;5;241m*\u001b[39margs, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, info_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 416\u001b[0m ):\n\u001b[1;32m 417\u001b[0m logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmethod\u001b[38;5;241m.\u001b[39mupper()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00margs\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mheaders\u001b[39m\u001b[38;5;124m'\u001b[39m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 418\u001b[0m status, headers, info, contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_request(\n\u001b[1;32m 419\u001b[0m method, path, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 420\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m json_out:\n\u001b[1;32m 422\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mloads(contents)\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/decorator.py:221\u001b[0m, in \u001b[0;36mdecorate..fun\u001b[0;34m(*args, **kw)\u001b[0m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m kwsyntax:\n\u001b[1;32m 220\u001b[0m args, kw \u001b[38;5;241m=\u001b[39m fix(args, kw, sig)\n\u001b[0;32m--> 221\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m caller(func, \u001b[38;5;241m*\u001b[39m(extras \u001b[38;5;241m+\u001b[39m args), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw)\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:114\u001b[0m, in \u001b[0;36mretry_request\u001b[0;34m(func, retries, *args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39msleep(\u001b[38;5;28mmin\u001b[39m(random\u001b[38;5;241m.\u001b[39mrandom() \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m (retry \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m), \u001b[38;5;241m32\u001b[39m))\n\u001b[0;32m--> 114\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 115\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\n\u001b[1;32m 116\u001b[0m HttpError,\n\u001b[1;32m 117\u001b[0m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 120\u001b[0m aiohttp\u001b[38;5;241m.\u001b[39mclient_exceptions\u001b[38;5;241m.\u001b[39mClientError,\n\u001b[1;32m 121\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 122\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 123\u001b[0m \u001b[38;5;28misinstance\u001b[39m(e, HttpError)\n\u001b[1;32m 124\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m e\u001b[38;5;241m.\u001b[39mcode \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m400\u001b[39m\n\u001b[1;32m 125\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrequester pays\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m e\u001b[38;5;241m.\u001b[39mmessage\n\u001b[1;32m 126\u001b[0m ):\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:411\u001b[0m, in \u001b[0;36mGCSFileSystem._request\u001b[0;34m(self, method, path, headers, json, data, *args, **kwargs)\u001b[0m\n\u001b[1;32m 408\u001b[0m info \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mrequest_info \u001b[38;5;66;03m# for debug only\u001b[39;00m\n\u001b[1;32m 409\u001b[0m contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m r\u001b[38;5;241m.\u001b[39mread()\n\u001b[0;32m--> 411\u001b[0m \u001b[43mvalidate_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstatus\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontents\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 412\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m status, headers, info, contents\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:83\u001b[0m, in \u001b[0;36mvalidate_response\u001b[0;34m(status, content, path, args)\u001b[0m\n\u001b[1;32m 81\u001b[0m path \u001b[38;5;241m=\u001b[39m path\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;241m*\u001b[39m[quote(p) \u001b[38;5;28;01mfor\u001b[39;00m p \u001b[38;5;129;01min\u001b[39;00m args])\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m404\u001b[39m:\n\u001b[0;32m---> 83\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(path)\n\u001b[1;32m 85\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(content, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdecode\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", + "\u001b[0;31mFileNotFoundError\u001b[0m: b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv" + ] + } + ], + "source": [ + "snps = adir1.snp_calls(region=\"KB672868:1000000-2000000\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/malariagen_data/__init__.py b/malariagen_data/__init__.py index dfa555aa7..6bc938825 100644 --- a/malariagen_data/__init__.py +++ b/malariagen_data/__init__.py @@ -1,5 +1,6 @@ # flake8: noqa from .af1 import Af1 +from .adir1 import Adir1 from .ag3 import Ag3 from .amin1 import Amin1 from .anopheles import AnophelesDataResource, Region diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py new file mode 100644 index 000000000..9b053ca62 --- /dev/null +++ b/malariagen_data/adir1.py @@ -0,0 +1,208 @@ +import sys + +import plotly.express as px # type: ignore + +import malariagen_data +from .anopheles import AnophelesDataResource + +MAJOR_VERSION_NUMBER = 1 +MAJOR_VERSION_PATH = "v1.x" +CONFIG_PATH = "v1.x-config.json" +GCS_DEFAULT_URL = "gs://vo_adir_production_us_central1/" +GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_production_us_central1/v1.x/staging" +GCS_REGION_URLS = { + "us-central1": "gs://vo_adir_production_us_central1", +} +# XPEHH_GWSS_CACHE_NAME = "adir1_xpehh_gwss_v1" +# IHS_GWSS_CACHE_NAME = "adir1_ihs_gwss_v1" + +TAXON_PALETTE = px.colors.qualitative.Plotly +TAXON_COLORS = { + "dirus": TAXON_PALETTE[0], +} + + +class Adir1(AnophelesDataResource): + """Provides access to data from Adir1.x releases. + + Parameters + ---------- + url : str, optional + Base path to data. Defaults to use Google Cloud Storage, or can + be a local path on your file system if data have been downloaded. + site_filters_analysis : str, optional + Site filters analysis version. + bokeh_output_notebook : bool, optional + If True (default), configure bokeh to output plots to the notebook. + results_cache : str, optional + Path to directory on local file system to save results. + log : str or stream, optional + File path or stream output for logging messages. + debug : bool, optional + Set to True to enable debug level logging. + show_progress : bool, optional + If True, show a progress bar during longer-running computations. The default can be overridden using an environmental variable named MGEN_SHOW_PROGRESS. + check_location : bool, optional + If True, use ipinfo to check the location of the client system. + **kwargs + Passed through to fsspec when setting up file system access. + + Examples + -------- + Access data from Google Cloud Storage (default): + + >>> import malariagen_data + >>> adir1 = malariagen_data.Adir1() + + Access data downloaded to a local file system: + + >>> adir1 = malariagen_data.Adir1("/local/path/to/vo_adir_release/") + + Access data from Google Cloud Storage, with caching on the local file system + in a directory named "gcs_cache": + + >>> adir1 = malariagen_data.Adir1( + ... "simplecache::gs://vo_adir_production_us_central1", + ... simplecache=dict(cache_storage="gcs_cache"), + ... ) + + Set up caching of some longer-running computations on the local file system, + in a directory named "results_cache": + + >>> adir1 = malariagen_data.Adir1(results_cache="results_cache") + + """ + + # _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME + # _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME + + def __init__( + self, + url=None, + bokeh_output_notebook=True, + results_cache=None, + log=sys.stdout, + debug=False, + show_progress=None, + check_location=True, + cohorts_analysis=None, + site_filters_analysis=None, + discordant_read_calls_analysis=None, + pre=False, + tqdm_class=None, + **storage_options, # used by fsspec via init_filesystem() + ): + super().__init__( + url=url, + config_path=CONFIG_PATH, + cohorts_analysis=cohorts_analysis, + aim_analysis=None, + aim_metadata_dtype=None, + aim_ids=None, + aim_palettes=None, + site_filters_analysis=site_filters_analysis, + discordant_read_calls_analysis=discordant_read_calls_analysis, + default_site_mask="funestus", + default_phasing_analysis="funestus", + default_coverage_calls_analysis="funestus", + bokeh_output_notebook=bokeh_output_notebook, + results_cache=results_cache, + log=log, + debug=debug, + show_progress=show_progress, + check_location=check_location, + pre=pre, + gcs_default_url=GCS_DEFAULT_URL, + gcs_region_urls=GCS_REGION_URLS, + major_version_number=MAJOR_VERSION_NUMBER, + major_version_path=MAJOR_VERSION_PATH, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + storage_options=storage_options, # used by fsspec via init_filesystem() + tqdm_class=tqdm_class, + taxon_colors=TAXON_COLORS, + virtual_contigs=None, + gene_names=None, + inversion_tag_path=None, + ) + + def __repr__(self): + text = ( + f"\n" + f"Storage URL : {self._url}\n" + f"Data releases available : {', '.join(self.releases)}\n" + f"Results cache : {self._results_cache}\n" + # f"Cohorts analysis : {self._cohorts_analysis}\n" + f"Site filters analysis : {self._site_filters_analysis}\n" + f"Software version : malariagen_data {malariagen_data.__version__}\n" + f"Client location : {self.client_location}\n" + f"---\n" + f"Please note that data are subject to terms of use,\n" + f"for more information see https://www.malariagen.net/data\n" + f"or contact support@malariagen.net. For API documentation see \n" + f"https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/Adir1.html" + ) + return text + + def _repr_html_(self): + html = f""" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
MalariaGEN Adir1 API client
+ Please note that data are subject to terms of use, + for more information see + the MalariaGEN website or contact support@malariagen.net. + See also the Adir1 API docs. +
+ Storage URL + {self._url}
+ Data releases available + {', '.join(self.releases)}
+ Results cache + {self._results_cache}
+ Cohorts analysis + {self._cohorts_analysis}
+ Site filters analysis + {self._site_filters_analysis}
+ Software version + malariagen_data {malariagen_data.__version__}
+ Client location + {self.client_location}
+ """ + return html From 624a21f3c38e70ea3968fe893dea1e8dd2caafd3 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 10 Jun 2025 15:03:15 +1000 Subject: [PATCH 08/41] add notebook exploring / troubleshooting adir1 --- notebooks/adir1_explore.ipynb | 483 ++++++++++++++++++++++++++++++++++ 1 file changed, 483 insertions(+) create mode 100644 notebooks/adir1_explore.ipynb diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb new file mode 100644 index 000000000..1fa71882d --- /dev/null +++ b/notebooks/adir1_explore.ipynb @@ -0,0 +1,483 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import malariagen_data" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "'use strict';\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " const force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + "const JS_MIME_TYPE = 'application/javascript';\n", + " const HTML_MIME_TYPE = 'text/html';\n", + " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " const CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " const script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\n", + " const cell = handle.cell;\n", + "\n", + " const id = cell.output_area._bokeh_element_id;\n", + " const server_id = cell.output_area._bokeh_server_id;\n", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(id)\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd_clean, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " const id = msg.content.text.trim()\n", + " drop(id)\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd_destroy);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " const output_area = handle.output_area;\n", + " const output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " const bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " const script_attrs = bk_div.children[0].attributes;\n", + " for (let i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " const toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"
    \\n\"+\n", + " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", + " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", + " \"
\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded(error = null) {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " const html = (() => {\n", + " if (typeof root.Bokeh === \"undefined\") {\n", + " if (error == null) {\n", + " return \"BokehJS is loading ...\";\n", + " } else {\n", + " return \"BokehJS failed to load.\";\n", + " }\n", + " } else {\n", + " const prefix = `BokehJS ${root.Bokeh.version}`;\n", + " if (error == null) {\n", + " return `${prefix} successfully loaded.`;\n", + " } else {\n", + " return `${prefix} encountered errors while loading and may not function as expected.`;\n", + " }\n", + " }\n", + " })();\n", + " el.innerHTML = html;\n", + "\n", + " if (error != null) {\n", + " const wrapper = document.createElement(\"div\");\n", + " wrapper.style.overflow = \"auto\";\n", + " wrapper.style.height = \"5em\";\n", + " wrapper.style.resize = \"vertical\";\n", + " const content = document.createElement(\"div\");\n", + " content.style.fontFamily = \"monospace\";\n", + " content.style.whiteSpace = \"pre-wrap\";\n", + " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", + " content.textContent = error.stack ?? error.toString();\n", + " wrapper.append(content);\n", + " el.append(wrapper);\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(() => display_loaded(error), 100);\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " try {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "\n", + " } catch (error) {throw error;\n", + " }} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
MalariaGEN Adir1 API client
\n", + " Please note that data are subject to terms of use,\n", + " for more information see \n", + " the MalariaGEN website or contact support@malariagen.net.\n", + " See also the Adir1 API docs.\n", + "
\n", + " Storage URL\n", + " gs://vo_adir_production_us_central1/
\n", + " Data releases available\n", + " 1.x
\n", + " Results cache\n", + " /Users/dennistpw/Projects/malariagen_results
\n", + " Cohorts analysis\n", + " noneyet
\n", + " Site filters analysis\n", + " sc_20250610
\n", + " Software version\n", + " malariagen_data 13.3.0.post33+90e72d5a
\n", + " Client location\n", + " Queensland, Australia
\n", + " " + ], + "text/plain": [ + "\n", + "Storage URL : gs://vo_adir_production_us_central1/\n", + "Data releases available : 1.x\n", + "Results cache : /Users/dennistpw/Projects/malariagen_results\n", + "Site filters analysis : sc_20250610\n", + "Software version : malariagen_data 13.3.0.post33+90e72d5a\n", + "Client location : Queensland, Australia\n", + "---\n", + "Please note that data are subject to terms of use,\n", + "for more information see https://www.malariagen.net/data\n", + "or contact support@malariagen.net. For API documentation see \n", + "https://malariagen.github.io/malariagen-data-python/v13.3.0.post33+90e72d5a/Adir1.html" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Init Adir1 API\n", + "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')\n", + "adir1" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + } + ], + "source": [ + "snps = adir1.snp_calls(region=\"KB672868:1000000-1010000\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", + "metadata": {}, + "outputs": [], + "source": [ + "adir1.pca(region = \"KB672868\", n_snps = 100_000, " + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From 6cbce3aeeb82b43fdd7888bca6fb33c570f83b2d Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 10 Jun 2025 15:21:09 +1000 Subject: [PATCH 09/41] comment out TOU lookups for metadata --- adir1_explore.ipynb | 451 ----------------------- malariagen_data/anoph/sample_metadata.py | 13 +- notebooks/adir1_explore.ipynb | 47 ++- 3 files changed, 50 insertions(+), 461 deletions(-) delete mode 100644 adir1_explore.ipynb diff --git a/adir1_explore.ipynb b/adir1_explore.ipynb deleted file mode 100644 index c42d93dd5..000000000 --- a/adir1_explore.ipynb +++ /dev/null @@ -1,451 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import malariagen_data" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "application/javascript": [ - "'use strict';\n", - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " const force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - "const JS_MIME_TYPE = 'application/javascript';\n", - " const HTML_MIME_TYPE = 'text/html';\n", - " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " const CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " const script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " function drop(id) {\n", - " const view = Bokeh.index.get_by_id(id)\n", - " if (view != null) {\n", - " view.model.document.clear()\n", - " Bokeh.index.delete(view)\n", - " }\n", - " }\n", - "\n", - " const cell = handle.cell;\n", - "\n", - " const id = cell.output_area._bokeh_element_id;\n", - " const server_id = cell.output_area._bokeh_server_id;\n", - "\n", - " // Clean up Bokeh references\n", - " if (id != null) {\n", - " drop(id)\n", - " }\n", - "\n", - " if (server_id !== undefined) {\n", - " // Clean up Bokeh references\n", - " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", - " cell.notebook.kernel.execute(cmd_clean, {\n", - " iopub: {\n", - " output: function(msg) {\n", - " const id = msg.content.text.trim()\n", - " drop(id)\n", - " }\n", - " }\n", - " });\n", - " // Destroy server and session\n", - " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", - " cell.notebook.kernel.execute(cmd_destroy);\n", - " }\n", - " }\n", - "\n", - " /**\n", - " * Handle when a new output is added\n", - " */\n", - " function handleAddOutput(event, handle) {\n", - " const output_area = handle.output_area;\n", - " const output = handle.output;\n", - "\n", - " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", - " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " const bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " const script_attrs = bk_div.children[0].attributes;\n", - " for (let i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", - " }\n", - " // store reference to server id on output_area\n", - " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", - " }\n", - " }\n", - "\n", - " function register_renderer(events, OutputArea) {\n", - "\n", - " function append_mime(data, metadata, element) {\n", - " // create a DOM node to render to\n", - " const toinsert = this.create_output_subarea(\n", - " metadata,\n", - " CLASS_NAME,\n", - " EXEC_MIME_TYPE\n", - " );\n", - " this.keyboard_manager.register_events(toinsert);\n", - " // Render to node\n", - " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", - " render(props, toinsert[toinsert.length - 1]);\n", - " element.append(toinsert);\n", - " return toinsert\n", - " }\n", - "\n", - " /* Handle when an output is cleared or removed */\n", - " events.on('clear_output.CodeCell', handleClearOutput);\n", - " events.on('delete.Cell', handleClearOutput);\n", - "\n", - " /* Handle when a new output is added */\n", - " events.on('output_added.OutputArea', handleAddOutput);\n", - "\n", - " /**\n", - " * Register the mime type and append_mime function with output_area\n", - " */\n", - " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", - " /* Is output safe? */\n", - " safe: true,\n", - " /* Index of renderer in `output_area.display_order` */\n", - " index: 0\n", - " });\n", - " }\n", - "\n", - " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", - " if (root.Jupyter !== undefined) {\n", - " const events = require('base/js/events');\n", - " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", - "\n", - " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", - " register_renderer(events, OutputArea);\n", - " }\n", - " }\n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", - " root._bokeh_timeout = Date.now() + 5000;\n", - " root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " const NB_LOAD_WARNING = {'data': {'text/html':\n", - " \"
\\n\"+\n", - " \"

\\n\"+\n", - " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", - " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", - " \"

\\n\"+\n", - " \"
    \\n\"+\n", - " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", - " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", - " \"
\\n\"+\n", - " \"\\n\"+\n", - " \"from bokeh.resources import INLINE\\n\"+\n", - " \"output_notebook(resources=INLINE)\\n\"+\n", - " \"\\n\"+\n", - " \"
\"}};\n", - "\n", - " function display_loaded(error = null) {\n", - " const el = document.getElementById(null);\n", - " if (el != null) {\n", - " const html = (() => {\n", - " if (typeof root.Bokeh === \"undefined\") {\n", - " if (error == null) {\n", - " return \"BokehJS is loading ...\";\n", - " } else {\n", - " return \"BokehJS failed to load.\";\n", - " }\n", - " } else {\n", - " const prefix = `BokehJS ${root.Bokeh.version}`;\n", - " if (error == null) {\n", - " return `${prefix} successfully loaded.`;\n", - " } else {\n", - " return `${prefix} encountered errors while loading and may not function as expected.`;\n", - " }\n", - " }\n", - " })();\n", - " el.innerHTML = html;\n", - "\n", - " if (error != null) {\n", - " const wrapper = document.createElement(\"div\");\n", - " wrapper.style.overflow = \"auto\";\n", - " wrapper.style.height = \"5em\";\n", - " wrapper.style.resize = \"vertical\";\n", - " const content = document.createElement(\"div\");\n", - " content.style.fontFamily = \"monospace\";\n", - " content.style.whiteSpace = \"pre-wrap\";\n", - " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", - " content.textContent = error.stack ?? error.toString();\n", - " wrapper.append(content);\n", - " el.append(wrapper);\n", - " }\n", - " } else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(() => display_loaded(error), 100);\n", - " }\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - "\n", - " function on_error(url) {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " for (let i = 0; i < css_urls.length; i++) {\n", - " const url = css_urls[i];\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " for (let i = 0; i < js_urls.length; i++) {\n", - " const url = js_urls[i];\n", - " const element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " };\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", - " const css_urls = [];\n", - "\n", - " const inline_js = [ function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - "function(Bokeh) {\n", - " }\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " if (root.Bokeh !== undefined || force === true) {\n", - " try {\n", - " for (let i = 0; i < inline_js.length; i++) {\n", - " inline_js[i].call(root, root.Bokeh);\n", - " }\n", - "\n", - " } catch (error) {throw error;\n", - " }} else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(run_inline_js, 100);\n", - " } else if (!root._bokeh_failed_load) {\n", - " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", - " root._bokeh_failed_load = true;\n", - " } else if (force !== true) {\n", - " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", - " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", - " }\n", - " }\n", - "\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(css_urls, js_urls, function() {\n", - " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(window));" - ], - "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "# Init API\n", - "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "f171c3b7-30c2-4e9f-9133-22206985de07", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "'KB672868'" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Are the contigs here? \n", - "chroms = adir1.contigs[:5]\n", - "chroms[1]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "ename": "FileNotFoundError", - "evalue": "b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:426\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 425\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_sets\u001b[49m\u001b[43m[\u001b[49m\u001b[43mrelease\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n", - "\u001b[0;31mKeyError\u001b[0m: '1.x'", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m snps \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msnp_calls\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868:1000000-2000000\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/snp_data.py:1007\u001b[0m, in \u001b[0;36mAnophelesSnpData.snp_calls\u001b[0;34m(self, region, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, inline_array, chunks, cohort_size, min_cohort_size, max_cohort_size, random_seed)\u001b[0m\n\u001b[1;32m 1001\u001b[0m base_params\u001b[38;5;241m.\u001b[39mvalidate_sample_selection_params(\n\u001b[1;32m 1002\u001b[0m sample_query\u001b[38;5;241m=\u001b[39msample_query, sample_indices\u001b[38;5;241m=\u001b[39msample_indices\n\u001b[1;32m 1003\u001b[0m )\n\u001b[1;32m 1005\u001b[0m \u001b[38;5;66;03m# Normalise parameters.\u001b[39;00m\n\u001b[1;32m 1006\u001b[0m sample_sets_prepped: Tuple[\u001b[38;5;28mstr\u001b[39m, \u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mtuple\u001b[39m(\n\u001b[0;32m-> 1007\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_sets_param\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1008\u001b[0m )\n\u001b[1;32m 1009\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m sample_sets\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_indices \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:524\u001b[0m, in \u001b[0;36mAnophelesBase._prep_sample_sets_param\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_prep_sample_sets_param\u001b[39m(\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets]\n\u001b[1;32m 519\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m List[\u001b[38;5;28mstr\u001b[39m]:\n\u001b[1;32m 520\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Common handling for the `sample_sets` parameter. For convenience, we\u001b[39;00m\n\u001b[1;32m 521\u001b[0m \u001b[38;5;124;03m allow this to be a single sample set, or a list of sample sets, or a\u001b[39;00m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;124;03m release identifier, or a list of release identifiers.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 524\u001b[0m all_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_list()\n\u001b[1;32m 526\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_sets \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 527\u001b[0m \u001b[38;5;66;03m# All available sample sets.\u001b[39;00m\n\u001b[1;32m 528\u001b[0m prepped_sample_sets \u001b[38;5;241m=\u001b[39m all_sample_sets\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets(release\u001b[38;5;241m=\u001b[39mr) \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrelease\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mr\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:430\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release]\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n\u001b[0;32m--> 430\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_sample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43msingle_release\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrelease\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 431\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release] \u001b[38;5;241m=\u001b[39m df\n\u001b[1;32m 433\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(release, Sequence):\n\u001b[1;32m 434\u001b[0m \u001b[38;5;66;03m# Ensure no duplicates.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:376\u001b[0m, in \u001b[0;36mAnophelesBase._read_sample_sets\u001b[0;34m(self, single_release)\u001b[0m\n\u001b[1;32m 373\u001b[0m manifest_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrelease_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/manifest.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 375\u001b[0m \u001b[38;5;66;03m# Read the manifest into a pandas dataframe.\u001b[39;00m\n\u001b[0;32m--> 376\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmanifest_path\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 377\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mread_csv(f, sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, na_values\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 379\u001b[0m \u001b[38;5;66;03m# Add a \"release\" column for convenience.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:218\u001b[0m, in \u001b[0;36mAnophelesBase.open_file\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_file\u001b[39m(\u001b[38;5;28mself\u001b[39m, path: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m IO:\n\u001b[1;32m 217\u001b[0m full_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_base_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 218\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfull_path\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1154\u001b[0m, in \u001b[0;36mAbstractFileSystem.open\u001b[0;34m(self, path, mode, block_size, cache_options, compression, **kwargs)\u001b[0m\n\u001b[1;32m 1152\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1153\u001b[0m ac \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mautocommit\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_intrans)\n\u001b[0;32m-> 1154\u001b[0m f \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_open\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1155\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1156\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1157\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1158\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mac\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1159\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1161\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfsspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcompression\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m compr\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1309\u001b[0m, in \u001b[0;36mGCSFileSystem._open\u001b[0;34m(self, path, mode, block_size, cache_options, acl, consistency, metadata, autocommit, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1307\u001b[0m block_size \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_block_size\n\u001b[1;32m 1308\u001b[0m const \u001b[38;5;241m=\u001b[39m consistency \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconsistency\n\u001b[0;32m-> 1309\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mGCSFile\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1311\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1312\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1313\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1314\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1315\u001b[0m \u001b[43m \u001b[49m\u001b[43mconsistency\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mconst\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1316\u001b[0m \u001b[43m \u001b[49m\u001b[43mmetadata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmetadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1317\u001b[0m \u001b[43m \u001b[49m\u001b[43macl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43macl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1318\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mautocommit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1319\u001b[0m \u001b[43m \u001b[49m\u001b[43mfixed_key_metadata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfixed_key_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1320\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1321\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1468\u001b[0m, in \u001b[0;36mGCSFile.__init__\u001b[0;34m(self, gcsfs, path, mode, block_size, autocommit, cache_type, cache_options, acl, consistency, metadata, content_type, timeout, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1466\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAttempt to open a bucket\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1467\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgeneration \u001b[38;5;241m=\u001b[39m _coalesce_generation(generation, path_generation)\n\u001b[0;32m-> 1468\u001b[0m \u001b[38;5;28;43msuper\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1469\u001b[0m \u001b[43m \u001b[49m\u001b[43mgcsfs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1470\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1471\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1472\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1473\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mautocommit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1474\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_type\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_type\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1475\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1476\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1477\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1478\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgcsfs \u001b[38;5;241m=\u001b[39m gcsfs\n\u001b[1;32m 1479\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mbucket \u001b[38;5;241m=\u001b[39m bucket\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1510\u001b[0m, in \u001b[0;36mAbstractBufferedFile.__init__\u001b[0;34m(self, fs, path, mode, block_size, autocommit, cache_type, cache_options, size, **kwargs)\u001b[0m\n\u001b[1;32m 1508\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m size\n\u001b[1;32m 1509\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1510\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdetails\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msize\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m 1511\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcache \u001b[38;5;241m=\u001b[39m caches[cache_type](\n\u001b[1;32m 1512\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mblocksize, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fetch_range, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mcache_options\n\u001b[1;32m 1513\u001b[0m )\n\u001b[1;32m 1514\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1504\u001b[0m, in \u001b[0;36mGCSFile.details\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1501\u001b[0m \u001b[38;5;129m@property\u001b[39m\n\u001b[1;32m 1502\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdetails\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[1;32m 1503\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 1504\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minfo\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgeneration\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneration\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1505\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:115\u001b[0m, in \u001b[0;36msync_wrapper..wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 114\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m obj \u001b[38;5;129;01mor\u001b[39;00m args[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 115\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloop\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:100\u001b[0m, in \u001b[0;36msync\u001b[0;34m(loop, func, timeout, *args, **kwargs)\u001b[0m\n\u001b[1;32m 98\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m FSTimeoutError \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mreturn_result\u001b[39;00m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(return_result, \u001b[38;5;167;01mBaseException\u001b[39;00m):\n\u001b[0;32m--> 100\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m return_result\n\u001b[1;32m 101\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 102\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m return_result\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:55\u001b[0m, in \u001b[0;36m_runner\u001b[0;34m(event, coro, result, timeout)\u001b[0m\n\u001b[1;32m 53\u001b[0m coro \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mwait_for(coro, timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m 54\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 55\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 56\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m ex:\n\u001b[1;32m 57\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m ex\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:797\u001b[0m, in \u001b[0;36mGCSFileSystem._info\u001b[0;34m(self, path, generation, **kwargs)\u001b[0m\n\u001b[1;32m 795\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 796\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdetail\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m \u001b[38;5;66;03m# Force to true for info\u001b[39;00m\n\u001b[0;32m--> 797\u001b[0m out \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ls(path, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 798\u001b[0m out0 \u001b[38;5;241m=\u001b[39m [o \u001b[38;5;28;01mfor\u001b[39;00m o \u001b[38;5;129;01min\u001b[39;00m out \u001b[38;5;28;01mif\u001b[39;00m o[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mrstrip(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m==\u001b[39m path]\n\u001b[1;32m 799\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m out0:\n\u001b[1;32m 800\u001b[0m \u001b[38;5;66;03m# exact hit\u001b[39;00m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:834\u001b[0m, in \u001b[0;36mGCSFileSystem._ls\u001b[0;34m(self, path, detail, prefix, versions, **kwargs)\u001b[0m\n\u001b[1;32m 832\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 833\u001b[0m out \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 834\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m entry \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_list_objects(\n\u001b[1;32m 835\u001b[0m path, prefix\u001b[38;5;241m=\u001b[39mprefix, versions\u001b[38;5;241m=\u001b[39mversions\n\u001b[1;32m 836\u001b[0m ):\n\u001b[1;32m 837\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m versions \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeneration\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m entry:\n\u001b[1;32m 838\u001b[0m entry \u001b[38;5;241m=\u001b[39m entry\u001b[38;5;241m.\u001b[39mcopy()\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:549\u001b[0m, in \u001b[0;36mGCSFileSystem._list_objects\u001b[0;34m(self, path, prefix, versions)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (items \u001b[38;5;241m+\u001b[39m pseudodirs):\n\u001b[1;32m 548\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m key:\n\u001b[0;32m--> 549\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_object(path)]\n\u001b[1;32m 550\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 551\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m []\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:491\u001b[0m, in \u001b[0;36mGCSFileSystem._get_object\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 488\u001b[0m \u001b[38;5;66;03m# Work around various permission settings. Prefer an object get (storage.objects.get), but\u001b[39;00m\n\u001b[1;32m 489\u001b[0m \u001b[38;5;66;03m# fall back to a bucket list + filter to object name (storage.objects.list).\u001b[39;00m\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 491\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_call(\n\u001b[1;32m 492\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGET\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/o/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, bucket, key, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, generation\u001b[38;5;241m=\u001b[39mgeneration\n\u001b[1;32m 493\u001b[0m )\n\u001b[1;32m 494\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 495\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(e)\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mForbidden\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:418\u001b[0m, in \u001b[0;36mGCSFileSystem._call\u001b[0;34m(self, method, path, json_out, info_out, *args, **kwargs)\u001b[0m\n\u001b[1;32m 414\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_call\u001b[39m(\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28mself\u001b[39m, method, path, \u001b[38;5;241m*\u001b[39margs, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, info_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 416\u001b[0m ):\n\u001b[1;32m 417\u001b[0m logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmethod\u001b[38;5;241m.\u001b[39mupper()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00margs\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mheaders\u001b[39m\u001b[38;5;124m'\u001b[39m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 418\u001b[0m status, headers, info, contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_request(\n\u001b[1;32m 419\u001b[0m method, path, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 420\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m json_out:\n\u001b[1;32m 422\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mloads(contents)\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/decorator.py:221\u001b[0m, in \u001b[0;36mdecorate..fun\u001b[0;34m(*args, **kw)\u001b[0m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m kwsyntax:\n\u001b[1;32m 220\u001b[0m args, kw \u001b[38;5;241m=\u001b[39m fix(args, kw, sig)\n\u001b[0;32m--> 221\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m caller(func, \u001b[38;5;241m*\u001b[39m(extras \u001b[38;5;241m+\u001b[39m args), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw)\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:114\u001b[0m, in \u001b[0;36mretry_request\u001b[0;34m(func, retries, *args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39msleep(\u001b[38;5;28mmin\u001b[39m(random\u001b[38;5;241m.\u001b[39mrandom() \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m (retry \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m), \u001b[38;5;241m32\u001b[39m))\n\u001b[0;32m--> 114\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 115\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\n\u001b[1;32m 116\u001b[0m HttpError,\n\u001b[1;32m 117\u001b[0m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 120\u001b[0m aiohttp\u001b[38;5;241m.\u001b[39mclient_exceptions\u001b[38;5;241m.\u001b[39mClientError,\n\u001b[1;32m 121\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 122\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 123\u001b[0m \u001b[38;5;28misinstance\u001b[39m(e, HttpError)\n\u001b[1;32m 124\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m e\u001b[38;5;241m.\u001b[39mcode \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m400\u001b[39m\n\u001b[1;32m 125\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrequester pays\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m e\u001b[38;5;241m.\u001b[39mmessage\n\u001b[1;32m 126\u001b[0m ):\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:411\u001b[0m, in \u001b[0;36mGCSFileSystem._request\u001b[0;34m(self, method, path, headers, json, data, *args, **kwargs)\u001b[0m\n\u001b[1;32m 408\u001b[0m info \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mrequest_info \u001b[38;5;66;03m# for debug only\u001b[39;00m\n\u001b[1;32m 409\u001b[0m contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m r\u001b[38;5;241m.\u001b[39mread()\n\u001b[0;32m--> 411\u001b[0m \u001b[43mvalidate_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstatus\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontents\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 412\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m status, headers, info, contents\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:83\u001b[0m, in \u001b[0;36mvalidate_response\u001b[0;34m(status, content, path, args)\u001b[0m\n\u001b[1;32m 81\u001b[0m path \u001b[38;5;241m=\u001b[39m path\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;241m*\u001b[39m[quote(p) \u001b[38;5;28;01mfor\u001b[39;00m p \u001b[38;5;129;01min\u001b[39;00m args])\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m404\u001b[39m:\n\u001b[0;32m---> 83\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(path)\n\u001b[1;32m 85\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(content, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdecode\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", - "\u001b[0;31mFileNotFoundError\u001b[0m: b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv" - ] - } - ], - "source": [ - "snps = adir1.snp_calls(region=\"KB672868:1000000-2000000\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index 62baa6870..c8bfbf601 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -180,15 +180,16 @@ def _parse_general_metadata( axis="columns", ) + # Have commented these out for now as a) this is not a public release and b) for some reason it breaks everything and I haven't had the time to work out why # Add study columns. - study_info = self.lookup_study_info(sample_set=sample_set) - for column in study_info: - df[column] = study_info[column] + # study_info = self.lookup_study_info(sample_set=sample_set) + # for column in study_info: + # df[column] = study_info[column] # Add terms-of-use columns. - terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) - for column in terms_of_use_info: - df[column] = terms_of_use_info[column] + # terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) + # for column in terms_of_use_info: + # df[column] = terms_of_use_info[column] return df diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb index 1fa71882d..450596a2f 100644 --- a/notebooks/adir1_explore.ipynb +++ b/notebooks/adir1_explore.ipynb @@ -450,12 +450,51 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + }, + { + "ename": "KeyError", + "evalue": "\"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:581\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 579\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 580\u001b[0m \u001b[38;5;66;03m# Attempt to retrieve from the cache.\u001b[39;00m\n\u001b[0;32m--> 581\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_metadata\u001b[49m\u001b[43m[\u001b[49m\u001b[43mcache_key\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n", + "\u001b[0;31mKeyError\u001b[0m: ('1276-AD-BD-ALAM-VMF00156', '1277-VO-KH-WITKOWSKI-VMF00151', '1277-VO-KH-WITKOWSKI-VMF00183', '1278-VO-TH-KOBYLINSKI-VMF00153')", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m100_000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:89\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 83\u001b[0m name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpca_v4\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;66;03m# Normalize params for consistent hash value.\u001b[39;00m\n\u001b[1;32m 86\u001b[0m (\n\u001b[1;32m 87\u001b[0m sample_sets_prepped,\n\u001b[1;32m 88\u001b[0m sample_indices_prepped,\n\u001b[0;32m---> 89\u001b[0m ) \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_selection_cache_params\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 90\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 91\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 93\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 94\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 95\u001b[0m region_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_region_cache_param(region\u001b[38;5;241m=\u001b[39mregion)\n\u001b[1;32m 96\u001b[0m site_mask_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_optional_site_mask_param(site_mask\u001b[38;5;241m=\u001b[39msite_mask)\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:892\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._prep_sample_selection_cache_params\u001b[0;34m(self, sample_sets, sample_query, sample_query_options, sample_indices)\u001b[0m\n\u001b[1;32m 885\u001b[0m sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_sample_sets_param(sample_sets\u001b[38;5;241m=\u001b[39msample_sets)\n\u001b[1;32m 887\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_query \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 888\u001b[0m \u001b[38;5;66;03m# Resolve query to a list of integers for more cache hits - we\u001b[39;00m\n\u001b[1;32m 889\u001b[0m \u001b[38;5;66;03m# do this because there are different ways to write the same pandas\u001b[39;00m\n\u001b[1;32m 890\u001b[0m \u001b[38;5;66;03m# query, and so it's better to evaluate the query and use a list of\u001b[39;00m\n\u001b[1;32m 891\u001b[0m \u001b[38;5;66;03m# integer indices instead.\u001b[39;00m\n\u001b[0;32m--> 892\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 893\u001b[0m sample_query_options \u001b[38;5;241m=\u001b[39m sample_query_options \u001b[38;5;129;01mor\u001b[39;00m {}\n\u001b[1;32m 894\u001b[0m loc_samples \u001b[38;5;241m=\u001b[39m df_samples\u001b[38;5;241m.\u001b[39meval(sample_query, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msample_query_options)\u001b[38;5;241m.\u001b[39mvalues\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:589\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 584\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_spinner(desc\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLoad sample metadata\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m 585\u001b[0m \u001b[38;5;66;03m## Build a single DataFrame using all available metadata.\u001b[39;00m\n\u001b[1;32m 586\u001b[0m \n\u001b[1;32m 587\u001b[0m \u001b[38;5;66;03m# Get the general sample metadata.\u001b[39;00m\n\u001b[1;32m 588\u001b[0m \u001b[38;5;66;03m# Note: this includes study and terms-of-use info.\u001b[39;00m\n\u001b[0;32m--> 589\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneral_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprepped_sample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[38;5;66;03m# Merge with the sequence QC metadata.\u001b[39;00m\n\u001b[1;32m 592\u001b[0m df_sequence_qc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequence_qc_metadata(\n\u001b[1;32m 593\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39mprepped_sample_sets\n\u001b[1;32m 594\u001b[0m )\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:185\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.general_metadata\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 175\u001b[0m \u001b[38;5;129m@doc\u001b[39m(\n\u001b[1;32m 176\u001b[0m summary\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28mself\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 184\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame:\n\u001b[0;32m--> 185\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_metadata_paths\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 186\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_template\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{release_path}\u001b[39;49;00m\u001b[38;5;124;43m/metadata/general/\u001b[39;49m\u001b[38;5;132;43;01m{sample_set}\u001b[39;49;00m\u001b[38;5;124;43m/samples.meta.csv\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 187\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_metadata_func\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_general_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 188\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:119\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_metadata_paths\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 117\u001b[0m path \u001b[38;5;241m=\u001b[39m file_paths[sample_set]\n\u001b[1;32m 118\u001b[0m data \u001b[38;5;241m=\u001b[39m files[path]\n\u001b[0;32m--> 119\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mparse_metadata_func\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 120\u001b[0m dfs\u001b[38;5;241m.\u001b[39mappend(df)\n\u001b[1;32m 122\u001b[0m \u001b[38;5;66;03m# Concatenate all DataFrames.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:160\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_general_metadata\u001b[0;34m(self, sample_set, data)\u001b[0m\n\u001b[1;32m 154\u001b[0m df[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mquarter\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m df\u001b[38;5;241m.\u001b[39mapply(\n\u001b[1;32m 155\u001b[0m \u001b[38;5;28;01mlambda\u001b[39;00m row: ((row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m3\u001b[39m) \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 156\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 157\u001b[0m )\n\u001b[1;32m 159\u001b[0m \u001b[38;5;66;03m# Add study columns.\u001b[39;00m\n\u001b[0;32m--> 160\u001b[0m study_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlookup_study_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_set\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m column \u001b[38;5;129;01min\u001b[39;00m study_info:\n\u001b[1;32m 162\u001b[0m df[column] \u001b[38;5;241m=\u001b[39m study_info[column]\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:487\u001b[0m, in \u001b[0;36mAnophelesBase.lookup_study_info\u001b[0;34m(self, sample_set)\u001b[0m\n\u001b[1;32m 485\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 486\u001b[0m df_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets()\u001b[38;5;241m.\u001b[39mset_index(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 487\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;241m=\u001b[39m \u001b[43mdf_sample_sets\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_url\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mto_dict(orient\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 491\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info[sample_set]\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/frame.py:3766\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 3764\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_iterator(key):\n\u001b[1;32m 3765\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 3766\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcolumns\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 3768\u001b[0m \u001b[38;5;66;03m# take() does not accept boolean indexers\u001b[39;00m\n\u001b[1;32m 3769\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(indexer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m==\u001b[39m \u001b[38;5;28mbool\u001b[39m:\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5935\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5933\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m use_interval_msg:\n\u001b[1;32m 5934\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[1;32m 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "\u001b[0;31mKeyError\u001b[0m: \"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"" + ] + } + ], "source": [ - "adir1.pca(region = \"KB672868\", n_snps = 100_000, " + "pca = adir1.pca(region = \"KB672868\", n_snps = 100_000, sample_query = \"country == 'Thailand'\")" ] } ], From fcbb281cdd7595d4fc06194f74e4a97aaeca55ea Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Thu, 12 Jun 2025 08:39:04 +1000 Subject: [PATCH 10/41] add annotation to commented out bit of metadata --- malariagen_data/anoph/sample_metadata.py | 34 +- notebooks/adir1_explore.ipynb | 522 ----------------------- 2 files changed, 18 insertions(+), 538 deletions(-) delete mode 100644 notebooks/adir1_explore.ipynb diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index c8bfbf601..399998524 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -618,29 +618,31 @@ def sample_metadata( # Note: this includes study and terms-of-use info. df_samples = self.general_metadata(sample_sets=prepped_sample_sets) + # Commented this out as it breaks some things - will fix + # Merge with the sequence QC metadata. - df_sequence_qc = self.sequence_qc_metadata( - sample_sets=prepped_sample_sets - ) + # df_sequence_qc = self.sequence_qc_metadata( + # sample_sets=prepped_sample_sets + # ) # Note: merging can change column dtypes - df_samples = df_samples.merge( - df_sequence_qc, on="sample_id", sort=False, how="left" - ) + # df_samples = df_samples.merge( + # df_sequence_qc, on="sample_id", sort=False, how="left" + # ) # If available, merge with the AIM metadata. - if self._aim_analysis: - df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) - df_samples = df_samples.merge( - df_aim, on="sample_id", sort=False, how="left" - ) + # if self._aim_analysis: + # df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) + # df_samples = df_samples.merge( + # df_aim, on="sample_id", sort=False, how="left" + # ) # If available, merge with the cohorts metadata. - if self._cohorts_analysis: - df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) - df_samples = df_samples.merge( - df_cohorts, on="sample_id", sort=False, how="left" - ) + # if self._cohorts_analysis: + # df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) + # df_samples = df_samples.merge( + # df_cohorts, on="sample_id", sort=False, how="left" + # ) # Store sample metadata in the cache. self._cache_sample_metadata[cache_key] = df_samples diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb deleted file mode 100644 index 450596a2f..000000000 --- a/notebooks/adir1_explore.ipynb +++ /dev/null @@ -1,522 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import malariagen_data" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "application/javascript": [ - "'use strict';\n", - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " const force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - "const JS_MIME_TYPE = 'application/javascript';\n", - " const HTML_MIME_TYPE = 'text/html';\n", - " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " const CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " const script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " function drop(id) {\n", - " const view = Bokeh.index.get_by_id(id)\n", - " if (view != null) {\n", - " view.model.document.clear()\n", - " Bokeh.index.delete(view)\n", - " }\n", - " }\n", - "\n", - " const cell = handle.cell;\n", - "\n", - " const id = cell.output_area._bokeh_element_id;\n", - " const server_id = cell.output_area._bokeh_server_id;\n", - "\n", - " // Clean up Bokeh references\n", - " if (id != null) {\n", - " drop(id)\n", - " }\n", - "\n", - " if (server_id !== undefined) {\n", - " // Clean up Bokeh references\n", - " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", - " cell.notebook.kernel.execute(cmd_clean, {\n", - " iopub: {\n", - " output: function(msg) {\n", - " const id = msg.content.text.trim()\n", - " drop(id)\n", - " }\n", - " }\n", - " });\n", - " // Destroy server and session\n", - " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", - " cell.notebook.kernel.execute(cmd_destroy);\n", - " }\n", - " }\n", - "\n", - " /**\n", - " * Handle when a new output is added\n", - " */\n", - " function handleAddOutput(event, handle) {\n", - " const output_area = handle.output_area;\n", - " const output = handle.output;\n", - "\n", - " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", - " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " const bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " const script_attrs = bk_div.children[0].attributes;\n", - " for (let i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " toinsert[toinsert.length - 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" root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " const NB_LOAD_WARNING = {'data': {'text/html':\n", - " \"
\\n\"+\n", - " \"

\\n\"+\n", - " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", - " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", - " \"

\\n\"+\n", - " \"
    \\n\"+\n", - " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", - " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", - " \"
\\n\"+\n", - " \"\\n\"+\n", - " \"from bokeh.resources import INLINE\\n\"+\n", - " \"output_notebook(resources=INLINE)\\n\"+\n", - " \"\\n\"+\n", - " \"
\"}};\n", - "\n", - " function display_loaded(error = null) {\n", - " const el = document.getElementById(null);\n", - " if (el != null) {\n", - " const html = (() => {\n", - " if (typeof root.Bokeh === \"undefined\") {\n", - " if (error == null) {\n", - " return \"BokehJS is loading ...\";\n", - " } else {\n", - " return \"BokehJS failed to load.\";\n", - " }\n", - " } else {\n", - " const prefix = `BokehJS ${root.Bokeh.version}`;\n", - " if (error == null) {\n", - " return `${prefix} successfully loaded.`;\n", - " } else {\n", - " return `${prefix} encountered errors while loading and may not function as expected.`;\n", - " }\n", - " }\n", - " })();\n", - " el.innerHTML = html;\n", - "\n", - " if (error != null) {\n", - " const wrapper = document.createElement(\"div\");\n", - " wrapper.style.overflow = \"auto\";\n", - " wrapper.style.height = \"5em\";\n", - " wrapper.style.resize = \"vertical\";\n", - " const content = document.createElement(\"div\");\n", - " content.style.fontFamily = \"monospace\";\n", - " content.style.whiteSpace = \"pre-wrap\";\n", - " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", - " content.textContent = error.stack ?? error.toString();\n", - " wrapper.append(content);\n", - " el.append(wrapper);\n", - " }\n", - " } else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(() => display_loaded(error), 100);\n", - " }\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - "\n", - " function on_error(url) {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " for (let i = 0; i < css_urls.length; i++) {\n", - " const url = css_urls[i];\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " for (let i = 0; i < js_urls.length; i++) {\n", - " const url = js_urls[i];\n", - " const element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " };\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", - " const css_urls = [];\n", - "\n", - " const inline_js = [ function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - "function(Bokeh) {\n", - " }\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " if (root.Bokeh !== undefined || force === true) {\n", - " try {\n", - " for (let i = 0; i < inline_js.length; i++) {\n", - " inline_js[i].call(root, root.Bokeh);\n", - " }\n", - "\n", - " } catch (error) {throw error;\n", - " }} else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(run_inline_js, 100);\n", - " } else if (!root._bokeh_failed_load) {\n", - " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", - " root._bokeh_failed_load = true;\n", - " } else if (force !== true) {\n", - " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", - " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", - " }\n", - " }\n", - "\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(css_urls, js_urls, function() {\n", - " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(window));" - ], - "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
MalariaGEN Adir1 API client
\n", - " Please note that data are subject to terms of use,\n", - " for more information see \n", - " the MalariaGEN website or contact support@malariagen.net.\n", - " See also the Adir1 API docs.\n", - "
\n", - " Storage URL\n", - " gs://vo_adir_production_us_central1/
\n", - " Data releases available\n", - " 1.x
\n", - " Results cache\n", - " /Users/dennistpw/Projects/malariagen_results
\n", - " Cohorts analysis\n", - " noneyet
\n", - " Site filters analysis\n", - " sc_20250610
\n", - " Software version\n", - " malariagen_data 13.3.0.post33+90e72d5a
\n", - " Client location\n", - " Queensland, Australia
\n", - " " - ], - "text/plain": [ - "\n", - "Storage URL : gs://vo_adir_production_us_central1/\n", - "Data releases available : 1.x\n", - "Results cache : /Users/dennistpw/Projects/malariagen_results\n", - "Site filters analysis : sc_20250610\n", - "Software version : malariagen_data 13.3.0.post33+90e72d5a\n", - "Client location : Queensland, Australia\n", - "---\n", - "Please note that data are subject to terms of use,\n", - "for more information see https://www.malariagen.net/data\n", - "or contact support@malariagen.net. For API documentation see \n", - "https://malariagen.github.io/malariagen-data-python/v13.3.0.post33+90e72d5a/Adir1.html" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Init Adir1 API\n", - "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')\n", - "adir1" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " \r" - ] - } - ], - "source": [ - "snps = adir1.snp_calls(region=\"KB672868:1000000-1010000\")" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " \r" - ] - }, - { - "ename": "KeyError", - "evalue": "\"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:581\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 579\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 580\u001b[0m \u001b[38;5;66;03m# Attempt to retrieve from the cache.\u001b[39;00m\n\u001b[0;32m--> 581\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_metadata\u001b[49m\u001b[43m[\u001b[49m\u001b[43mcache_key\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n", - "\u001b[0;31mKeyError\u001b[0m: ('1276-AD-BD-ALAM-VMF00156', '1277-VO-KH-WITKOWSKI-VMF00151', '1277-VO-KH-WITKOWSKI-VMF00183', '1278-VO-TH-KOBYLINSKI-VMF00153')", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m100_000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:89\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 83\u001b[0m name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpca_v4\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;66;03m# Normalize params for consistent hash value.\u001b[39;00m\n\u001b[1;32m 86\u001b[0m (\n\u001b[1;32m 87\u001b[0m sample_sets_prepped,\n\u001b[1;32m 88\u001b[0m sample_indices_prepped,\n\u001b[0;32m---> 89\u001b[0m ) \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_selection_cache_params\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 90\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 91\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 93\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 94\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 95\u001b[0m region_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_region_cache_param(region\u001b[38;5;241m=\u001b[39mregion)\n\u001b[1;32m 96\u001b[0m site_mask_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_optional_site_mask_param(site_mask\u001b[38;5;241m=\u001b[39msite_mask)\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:892\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._prep_sample_selection_cache_params\u001b[0;34m(self, sample_sets, sample_query, sample_query_options, sample_indices)\u001b[0m\n\u001b[1;32m 885\u001b[0m sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_sample_sets_param(sample_sets\u001b[38;5;241m=\u001b[39msample_sets)\n\u001b[1;32m 887\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_query \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 888\u001b[0m \u001b[38;5;66;03m# Resolve query to a list of integers for more cache hits - we\u001b[39;00m\n\u001b[1;32m 889\u001b[0m \u001b[38;5;66;03m# do this because there are different ways to write the same pandas\u001b[39;00m\n\u001b[1;32m 890\u001b[0m \u001b[38;5;66;03m# query, and so it's better to evaluate the query and use a list of\u001b[39;00m\n\u001b[1;32m 891\u001b[0m \u001b[38;5;66;03m# integer indices instead.\u001b[39;00m\n\u001b[0;32m--> 892\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 893\u001b[0m sample_query_options \u001b[38;5;241m=\u001b[39m sample_query_options \u001b[38;5;129;01mor\u001b[39;00m {}\n\u001b[1;32m 894\u001b[0m loc_samples \u001b[38;5;241m=\u001b[39m df_samples\u001b[38;5;241m.\u001b[39meval(sample_query, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msample_query_options)\u001b[38;5;241m.\u001b[39mvalues\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:589\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 584\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_spinner(desc\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLoad sample metadata\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m 585\u001b[0m \u001b[38;5;66;03m## Build a single DataFrame using all available metadata.\u001b[39;00m\n\u001b[1;32m 586\u001b[0m \n\u001b[1;32m 587\u001b[0m \u001b[38;5;66;03m# Get the general sample metadata.\u001b[39;00m\n\u001b[1;32m 588\u001b[0m \u001b[38;5;66;03m# Note: this includes study and terms-of-use info.\u001b[39;00m\n\u001b[0;32m--> 589\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneral_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprepped_sample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[38;5;66;03m# Merge with the sequence QC metadata.\u001b[39;00m\n\u001b[1;32m 592\u001b[0m df_sequence_qc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequence_qc_metadata(\n\u001b[1;32m 593\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39mprepped_sample_sets\n\u001b[1;32m 594\u001b[0m )\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:185\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.general_metadata\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 175\u001b[0m \u001b[38;5;129m@doc\u001b[39m(\n\u001b[1;32m 176\u001b[0m summary\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28mself\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 184\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame:\n\u001b[0;32m--> 185\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_metadata_paths\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 186\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_template\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{release_path}\u001b[39;49;00m\u001b[38;5;124;43m/metadata/general/\u001b[39;49m\u001b[38;5;132;43;01m{sample_set}\u001b[39;49;00m\u001b[38;5;124;43m/samples.meta.csv\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 187\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_metadata_func\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_general_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 188\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:119\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_metadata_paths\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 117\u001b[0m path \u001b[38;5;241m=\u001b[39m file_paths[sample_set]\n\u001b[1;32m 118\u001b[0m data \u001b[38;5;241m=\u001b[39m files[path]\n\u001b[0;32m--> 119\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mparse_metadata_func\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 120\u001b[0m dfs\u001b[38;5;241m.\u001b[39mappend(df)\n\u001b[1;32m 122\u001b[0m \u001b[38;5;66;03m# Concatenate all DataFrames.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:160\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_general_metadata\u001b[0;34m(self, sample_set, data)\u001b[0m\n\u001b[1;32m 154\u001b[0m df[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mquarter\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m df\u001b[38;5;241m.\u001b[39mapply(\n\u001b[1;32m 155\u001b[0m \u001b[38;5;28;01mlambda\u001b[39;00m row: ((row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m3\u001b[39m) \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 156\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 157\u001b[0m )\n\u001b[1;32m 159\u001b[0m \u001b[38;5;66;03m# Add study columns.\u001b[39;00m\n\u001b[0;32m--> 160\u001b[0m study_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlookup_study_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_set\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m column \u001b[38;5;129;01min\u001b[39;00m study_info:\n\u001b[1;32m 162\u001b[0m df[column] \u001b[38;5;241m=\u001b[39m study_info[column]\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:487\u001b[0m, in \u001b[0;36mAnophelesBase.lookup_study_info\u001b[0;34m(self, sample_set)\u001b[0m\n\u001b[1;32m 485\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 486\u001b[0m df_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets()\u001b[38;5;241m.\u001b[39mset_index(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 487\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;241m=\u001b[39m \u001b[43mdf_sample_sets\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_url\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mto_dict(orient\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 491\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info[sample_set]\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/frame.py:3766\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 3764\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_iterator(key):\n\u001b[1;32m 3765\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 3766\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcolumns\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 3768\u001b[0m \u001b[38;5;66;03m# take() does not accept boolean indexers\u001b[39;00m\n\u001b[1;32m 3769\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(indexer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m==\u001b[39m \u001b[38;5;28mbool\u001b[39m:\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5935\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5933\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m use_interval_msg:\n\u001b[1;32m 5934\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[1;32m 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", - "\u001b[0;31mKeyError\u001b[0m: \"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"" - ] - } - ], - "source": [ - "pca = adir1.pca(region = \"KB672868\", n_snps = 100_000, sample_query = \"country == 'Thailand'\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} From ce7b80a84f93951a7b4918f9ee3870615fce442d Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Sun, 15 Jun 2025 22:28:15 -0500 Subject: [PATCH 11/41] forgot how the alphabet works d'oh --- malariagen_data/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/__init__.py b/malariagen_data/__init__.py index 6bc938825..306896658 100644 --- a/malariagen_data/__init__.py +++ b/malariagen_data/__init__.py @@ -1,6 +1,6 @@ # flake8: noqa -from .af1 import Af1 from .adir1 import Adir1 +from .af1 import Af1 from .ag3 import Ag3 from .amin1 import Amin1 from .anopheles import AnophelesDataResource, Region From 1b196344fb4f7cd1e4e836b52440b22610cf2df3 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Mon, 16 Jun 2025 20:35:38 -0500 Subject: [PATCH 12/41] add hashing to roh function --- malariagen_data/adir1.py | 6 +- malariagen_data/anopheles.py | 71 +- poetry.lock | 3689 ++++++++++++++++++---------------- pyproject.toml | 1 + 4 files changed, 2031 insertions(+), 1736 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index 9b053ca62..c24562426 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -102,9 +102,9 @@ def __init__( aim_palettes=None, site_filters_analysis=site_filters_analysis, discordant_read_calls_analysis=discordant_read_calls_analysis, - default_site_mask="funestus", - default_phasing_analysis="funestus", - default_coverage_calls_analysis="funestus", + default_site_mask="dirus", + default_phasing_analysis="dirus", + default_coverage_calls_analysis="dirus", bokeh_output_notebook=bokeh_output_notebook, results_cache=results_cache, log=log, diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py index ed9cb65cf..7fc78451e 100644 --- a/malariagen_data/anopheles.py +++ b/malariagen_data/anopheles.py @@ -574,31 +574,68 @@ def roh_hmm( debug = self._log.debug resolved_region: Region = parse_single_region(self, region) - del region - debug("compute windowed heterozygosity") - sample_id, sample_set, windows, counts = self._sample_count_het( + name = "roh" + + params = dict( sample=sample, - region=resolved_region, - site_mask=site_mask, + region=region, window_size=window_size, + site_mask=site_mask, sample_set=sample_set, - chunks=chunks, - inline_array=inline_array, - ) - - debug("compute runs of homozygosity") - df_roh = self._roh_hmm_predict( - windows=windows, - counts=counts, phet_roh=phet_roh, phet_nonroh=phet_nonroh, transition=transition, - window_size=window_size, - sample_id=sample_id, - contig=resolved_region.contig, + chunks=chunks, + inline_array=inline_array, ) + del region + + try: + # Load cached numeric data, adding str / obj data again. + results = self.results_cache_get(name=name, params=params) + df_roh = pd.DataFrame(results) + df_roh["sample_id"] = sample + df_roh["contig"] = resolved_region.contig + + except CacheMiss: + debug("compute windowed heterozygosity") + sample_id, sample_set, windows, counts = self._sample_count_het( + sample=sample, + region=resolved_region, + site_mask=site_mask, + window_size=window_size, + sample_set=sample_set, + chunks=chunks, + inline_array=inline_array, + ) + + debug("compute runs of homozygosity") + df_roh = self._roh_hmm_predict( + windows=windows, + counts=counts, + phet_roh=phet_roh, + phet_nonroh=phet_nonroh, + transition=transition, + window_size=window_size, + sample_id=sample_id, + contig=resolved_region.contig, + ) + + # Specify numeric columns to save (saving obj - sample ID and contig - breaks the save. + columns_to_save = [ + "roh_start", + "roh_stop", + "roh_length", + "roh_is_marginal", + ] + self.results_cache_set( + name=name, + params=params, + results={col: df_roh[col].to_numpy() for col in columns_to_save}, + ) + return df_roh @check_types @@ -1306,7 +1343,7 @@ def ihs_gwss( ) -> Tuple[np.ndarray, np.ndarray]: # change this name if you ever change the behaviour of this function, to # invalidate any previously cached data - name = self._ihs_gwss_cache_name + name = "roh" params = dict( contig=contig, diff --git a/poetry.lock b/poetry.lock index 7ea703765..d02d5c5bc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. [[package]] name = "accessible-pygments" @@ -6,6 +6,8 @@ version = "0.0.5" description = "A collection of accessible pygments styles" optional = false python-versions = ">=3.9" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"}, {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"}, @@ -20,127 +22,122 @@ tests = ["hypothesis", "pytest"] [[package]] name = "aiobotocore" -version = "2.21.1" +version = "2.15.2" description = "Async client for aws services using botocore and aiohttp" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ - {file = "aiobotocore-2.21.1-py3-none-any.whl", hash = "sha256:bd7c49a6d6f8a3d9444b0a94417c8da13813b5c7eec1c4f0ec2db7e8ce8f23e7"}, - {file = "aiobotocore-2.21.1.tar.gz", hash = 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"Operations with ISO 8601 durations" optional = false python-versions = ">=3.7" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"}, {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"}, @@ -2009,6 +2114,7 @@ version = "2.2.0" description = "Safely pass data to untrusted environments and back." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "itsdangerous-2.2.0-py3-none-any.whl", hash = "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef"}, {file = "itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173"}, @@ -2020,6 +2126,7 @@ version = "0.19.2" description = "An autocompletion tool for Python that can be used for text editors." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"}, {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"}, @@ -2035,13 +2142,14 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"] [[package]] name = "jinja2" -version = "3.1.6" +version = "3.1.4" description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" +groups = ["main"] files = [ - {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"}, - {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"}, + {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"}, + {file = "jinja2-3.1.4.tar.gz", hash = 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(==24.3.1)", "pylint (==3.2.3)", "ruff (==0.7.3)", "twine (==5.1.1)", "uv (==0.5.1)"] [[package]] name = "jsonpointer" @@ -2092,6 +2204,8 @@ version = "3.0.0" description = "Identify specific nodes in a JSON document (RFC 6901)" optional = false python-versions = ">=3.7" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942"}, {file = "jsonpointer-3.0.0.tar.gz", hash = "sha256:2b2d729f2091522d61c3b31f82e11870f60b68f43fbc705cb76bf4b832af59ef"}, @@ -2103,6 +2217,8 @@ version = "4.23.0" description = "An implementation of JSON Schema validation for Python" optional = false python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"}, {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"}, @@ -2132,6 +2248,8 @@ version = "2024.10.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" optional = false python-versions = ">=3.9" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jsonschema_specifications-2024.10.1-py3-none-any.whl", hash = "sha256:a09a0680616357d9a0ecf05c12ad234479f549239d0f5b55f3deea67475da9bf"}, {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"}, @@ -2146,6 +2264,7 @@ version = "8.6.3" description = "Jupyter protocol implementation and client libraries" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"}, {file = "jupyter_client-8.6.3.tar.gz", hash = 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A base package on which Jupyter projects rely." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"}, {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"}, @@ -2184,18 +2304,19 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout" [[package]] name = "jupyter-events" -version = "0.12.0" +version = "0.10.0" description = "Jupyter Event System library" optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ - {file = "jupyter_events-0.12.0-py3-none-any.whl", hash = "sha256:6464b2fa5ad10451c3d35fabc75eab39556ae1e2853ad0c0cc31b656731a97fb"}, - {file = "jupyter_events-0.12.0.tar.gz", hash = "sha256:fc3fce98865f6784c9cd0a56a20644fc6098f21c8c33834a8d9fe383c17e554b"}, + {file = 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">=3.8" +groups = ["main"] files = [ {file = "jupyter_leaflet-0.19.2-py3-none-any.whl", hash = "sha256:0d57e15e80c08a4360f0cde0b4c490beddc5d422bb0e9bc1c0b4479d3fb725a6"}, {file = "jupyter_leaflet-0.19.2.tar.gz", hash = "sha256:b09b5ba48b1488cb61da37a6f558347269eb53ff6d64dc1a73e005ffc4420063"}, @@ -2225,6 +2347,8 @@ version = "2.2.5" description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server" optional = false python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"}, {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"}, @@ -2235,13 +2359,15 @@ jupyter-server = ">=1.1.2" [[package]] name = "jupyter-server" -version = "2.15.0" +version = "2.14.2" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ - {file = "jupyter_server-2.15.0-py3-none-any.whl", hash = "sha256:872d989becf83517012ee669f09604aa4a28097c0bd90b2f424310156c2cdae3"}, - {file = "jupyter_server-2.15.0.tar.gz", hash = "sha256:9d446b8697b4f7337a1b7cdcac40778babdd93ba614b6d68ab1c0c918f1c4084"}, + {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"}, + {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"}, ] [package.dependencies] @@ -2250,7 +2376,7 @@ argon2-cffi = ">=21.1" jinja2 = ">=3.0.3" jupyter-client = ">=7.4.4" jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" -jupyter-events = ">=0.11.0" +jupyter-events = ">=0.9.0" jupyter-server-terminals = ">=0.4.4" nbconvert = ">=6.4.4" nbformat = ">=5.3.0" @@ -2275,6 +2401,8 @@ version = "0.5.3" description = "A Jupyter Server Extension Providing Terminals." optional = false python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jupyter_server_terminals-0.5.3-py3-none-any.whl", hash = "sha256:41ee0d7dc0ebf2809c668e0fc726dfaf258fcd3e769568996ca731b6194ae9aa"}, {file = "jupyter_server_terminals-0.5.3.tar.gz", hash = "sha256:5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269"}, @@ -2290,18 +2418,20 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (> [[package]] name = "jupyterlab" -version = "4.4.0" +version = "4.3.2" description = "JupyterLab computational environment" optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ - {file = "jupyterlab-4.4.0-py3-none-any.whl", hash = "sha256:61d33991fbb352cc7caac08bd0c34577fea86d8d5d9772600d9d5a6bcbc882c0"}, - {file = "jupyterlab-4.4.0.tar.gz", hash = "sha256:f1767d5f0104e40f3b4a63bf6892bbef8e4704dcabf0c78408a3bdc411792f04"}, + {file = "jupyterlab-4.3.2-py3-none-any.whl", hash = "sha256:e87100cbab8b886ff7a4f325c856100ba6fdfe916162a85409daf0e707e19d1d"}, + {file = "jupyterlab-4.3.2.tar.gz", hash = "sha256:3c0a6882dbddcc0a7bfdd5e2236f351b2b263e48780236e6996c2aca13ac5b22"}, ] [package.dependencies] async-lru = ">=1.0.0" -httpx = ">=0.25.0" +httpx = ">=0.28.0,<0.29.0" ipykernel = ">=6.5.0" jinja2 = ">=3.0.3" jupyter-core = "*" @@ -2310,15 +2440,15 @@ jupyter-server = ">=2.4.0,<3" jupyterlab-server = ">=2.27.1,<3" notebook-shim = ">=0.2" packaging = "*" -setuptools = ">=41.1.0" +setuptools = ">=40.8.0" tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""} tornado = ">=6.2.0" traitlets = "*" [package.extras] -dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.9.9)"] -docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", 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["pytest-enabler (>=2.2)"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] [extras] dev = ["jupyterlab", "memory-profiler", "mypy", "notebook", "pandas-stubs", "pre-commit", "pydata-sphinx-theme", "pytest", "pytest-cases", "pytest-cov", "pytest-xdist", "ruff", "snakeviz", "sphinx", "sphinx_design"] [metadata] -lock-version = "2.0" +lock-version = "2.1" python-versions = ">=3.10,<3.13" -content-hash = "b1fb6dbca8e75ab7da9028a4d6ff87d1cabe31f69690245cb915554844deb6a9" +content-hash = "e2dc0c54942b1e2261de9c28a0c3750350ff2bb6aa20700a71ec8fba81e1382a" diff --git a/pyproject.toml b/pyproject.toml index 8e908a1d8..b79742199 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -92,6 +92,7 @@ sphinx = "*" pydata-sphinx-theme = "*" sphinx_design = "*" pandas-stubs = "*" +ipykernel = "^6.29.5" [tool.poetry.extras] dev = ["pytest", "pytest-xdist", "pytest-cases", "pytest-cov", "notebook", "jupyterlab", "pre-commit", "ruff", "snakeviz", "mypy", "memory-profiler", "sphinx", "pydata-sphinx-theme", "sphinx_design", "pandas-stubs"] From 6320047f044d1adda73ddecea35cfe9ccbbf0ce3 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 17 Jun 2025 22:52:24 -0500 Subject: [PATCH 13/41] reintroduce cohorts, aims, qc to metadata --- malariagen_data/adir1.py | 2 ++ malariagen_data/anoph/sample_metadata.py | 32 ++++++++++++------------ malariagen_data/anopheles.py | 13 +++++++++- poetry.lock | 2 +- 4 files changed, 31 insertions(+), 18 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index c24562426..92709eeb4 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -79,6 +79,7 @@ class Adir1(AnophelesDataResource): def __init__( self, url=None, + public_url=GCS_DEFAULT_PUBLIC_URL, bokeh_output_notebook=True, results_cache=None, log=sys.stdout, @@ -94,6 +95,7 @@ def __init__( ): super().__init__( url=url, + public_url=public_url, config_path=CONFIG_PATH, cohorts_analysis=cohorts_analysis, aim_analysis=None, diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index 399998524..fd98270c4 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -621,28 +621,28 @@ def sample_metadata( # Commented this out as it breaks some things - will fix # Merge with the sequence QC metadata. - # df_sequence_qc = self.sequence_qc_metadata( - # sample_sets=prepped_sample_sets - # ) + df_sequence_qc = self.sequence_qc_metadata( + sample_sets=prepped_sample_sets + ) # Note: merging can change column dtypes - # df_samples = df_samples.merge( - # df_sequence_qc, on="sample_id", sort=False, how="left" - # ) + df_samples = df_samples.merge( + df_sequence_qc, on="sample_id", sort=False, how="left" + ) # If available, merge with the AIM metadata. - # if self._aim_analysis: - # df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) - # df_samples = df_samples.merge( - # df_aim, on="sample_id", sort=False, how="left" - # ) + if self._aim_analysis: + df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) + df_samples = df_samples.merge( + df_aim, on="sample_id", sort=False, how="left" + ) # If available, merge with the cohorts metadata. - # if self._cohorts_analysis: - # df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) - # df_samples = df_samples.merge( - # df_cohorts, on="sample_id", sort=False, how="left" - # ) + if self._cohorts_analysis: + df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) + df_samples = df_samples.merge( + df_cohorts, on="sample_id", sort=False, how="left" + ) # Store sample metadata in the cache. self._cache_sample_metadata[cache_key] = df_samples diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py index 7fc78451e..94ebc488b 100644 --- a/malariagen_data/anopheles.py +++ b/malariagen_data/anopheles.py @@ -595,7 +595,17 @@ def roh_hmm( try: # Load cached numeric data, adding str / obj data again. results = self.results_cache_get(name=name, params=params) - df_roh = pd.DataFrame(results) + + # Reconstruct dataframe + df_roh = pd.DataFrame( + { + "roh_start": results["roh_start"], + "roh_stop": results["roh_stop"], + "roh_length": results["roh_length"], + "roh_is_marginal": results["roh_is_marginal"], + } + ) + df_roh["sample_id"] = sample df_roh["contig"] = resolved_region.contig @@ -630,6 +640,7 @@ def roh_hmm( "roh_length", "roh_is_marginal", ] + self.results_cache_set( name=name, params=params, diff --git a/poetry.lock b/poetry.lock index d02d5c5bc..e9450b337 100644 --- a/poetry.lock +++ b/poetry.lock @@ -5854,4 +5854,4 @@ dev = ["jupyterlab", "memory-profiler", "mypy", "notebook", "pandas-stubs", "pre [metadata] lock-version = "2.1" python-versions = ">=3.10,<3.13" -content-hash = "e2dc0c54942b1e2261de9c28a0c3750350ff2bb6aa20700a71ec8fba81e1382a" +content-hash = "72db9c739659d268f984ad2d5b8f3593a41be1469e6b7599afed28c95293bb46" From 5cd669f271e893ec207995cfc25967c76e39b78d Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Thu, 10 Jul 2025 01:33:15 -0500 Subject: [PATCH 14/41] add cohorts analysis --- malariagen_data/adir1.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index 92709eeb4..63e383d50 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -135,7 +135,7 @@ def __repr__(self): f"Storage URL : {self._url}\n" f"Data releases available : {', '.join(self.releases)}\n" f"Results cache : {self._results_cache}\n" - # f"Cohorts analysis : {self._cohorts_analysis}\n" + f"Cohorts analysis : {self._cohorts_analysis}\n" f"Site filters analysis : {self._site_filters_analysis}\n" f"Software version : malariagen_data {malariagen_data.__version__}\n" f"Client location : {self.client_location}\n" From 0a9c07ce5c46fc0bec370e33f6043aa16adfeacc Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Sun, 28 Sep 2025 01:48:39 -0500 Subject: [PATCH 15/41] QC data now being built with metadata Had commented this out, back now! --- malariagen_data/anoph/sample_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index fd98270c4..bba958fa4 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -349,7 +349,7 @@ def sequence_qc_metadata( self, sample_sets: Optional[base_params.sample_sets] = None ) -> pd.DataFrame: return self._parse_metadata_paths( - path_template="{release_path}/metadata/curation/{sample_set}/sequence_qc_stats.csv", + path_template="{release_path}/metadata/general/{sample_set}/sequence_qc_stats.csv", parse_metadata_func=self._parse_sequence_qc_metadata, sample_sets=sample_sets, ) From 9a3ec96f1e91f8e4cb72804c171bca014f0a267b Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Sun, 28 Sep 2025 01:50:45 -0500 Subject: [PATCH 16/41] QC metadata back in now --- malariagen_data/anoph/sample_metadata.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index bba958fa4..67145b337 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -618,8 +618,6 @@ def sample_metadata( # Note: this includes study and terms-of-use info. df_samples = self.general_metadata(sample_sets=prepped_sample_sets) - # Commented this out as it breaks some things - will fix - # Merge with the sequence QC metadata. df_sequence_qc = self.sequence_qc_metadata( sample_sets=prepped_sample_sets From fb8a42efd33c2cef08db5b3e92c481ac0c01bbd3 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 7 Oct 2025 19:52:53 -0500 Subject: [PATCH 17/41] Update adir1.py --- malariagen_data/adir1.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index 63e383d50..00dd3a6e1 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -23,7 +23,7 @@ class Adir1(AnophelesDataResource): - """Provides access to data from Adir1.x releases. + """Provides access to data from Adir1.0 releases. Parameters ---------- From 6fa3c638198a1a77db890109d3a7c0bfdf6fffc6 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Fri, 10 Oct 2025 10:12:17 +1000 Subject: [PATCH 18/41] Add Adir1 docs page, add index entry (docs contain all functions minus hap/cnv/aim data) --- docs/source/Adir1.rst | 150 ++++++++++++++++++++++++++++++++++++++++++ docs/source/index.rst | 8 +++ 2 files changed, 158 insertions(+) create mode 100644 docs/source/Adir1.rst diff --git a/docs/source/Adir1.rst b/docs/source/Adir1.rst new file mode 100644 index 000000000..ada72d451 --- /dev/null +++ b/docs/source/Adir1.rst @@ -0,0 +1,150 @@ +Adir1 +===== + +This page provides a curated list of functions and properties available in the ``malariagen_data`` API +for data on mosquitoes from the *Anopheles dirus* complex. + +To set up the API, use the following code:: + + import malariagen_data + adir1 = malariagen_data.Adir1() + +All the functions below can then be accessed as methods on the ``adir1`` object. E.g., to call the +``sample_metadata()`` function, do:: + + df_samples = adir1.sample_metadata() + +For more information about the data and terms of use, please see the +`MalariaGEN website `_ or contact support@malariagen.net. + +.. currentmodule:: malariagen_data.adir1.Adir1 + +Basic data access +----------------- +.. autosummary:: + :toctree: generated/ + + releases + sample_sets + lookup_release + lookup_study + +Reference genome data access +---------------------------- +.. autosummary:: + :toctree: generated/ + + contigs + genome_sequence + genome_features + plot_transcript + plot_genes + +Sample metadata access +---------------------- +.. autosummary:: + :toctree: generated/ + + sample_metadata + add_extra_metadata + clear_extra_metadata + lookup_sample + count_samples + plot_samples_bar + plot_samples_interactive_map + plot_sample_location_mapbox + plot_sample_location_geo + wgs_data_catalog + cohorts + +SNP data access +--------------- +.. autosummary:: + :toctree: generated/ + + site_mask_ids + snp_calls + snp_allele_counts + plot_snps + site_annotations + is_accessible + biallelic_snp_calls + biallelic_diplotypes + biallelic_snps_to_plink + +Integrative genomics viewer (IGV) +--------------------------------- +.. autosummary:: + :toctree: generated/ + + igv + view_alignments + +SNP frequency analysis +---------------------- +.. autosummary:: + :toctree: generated/ + + snp_allele_frequencies + snp_allele_frequencies_advanced + aa_allele_frequencies + aa_allele_frequencies_advanced + plot_frequencies_heatmap + plot_frequencies_time_series + plot_frequencies_interactive_map + +Principal components analysis (PCA) +----------------------------------- +.. autosummary:: + :toctree: generated/ + + pca + plot_pca_variance + plot_pca_coords + plot_pca_coords_3d + +Genetic distance and neighbour-joining trees (NJT) +-------------------------------------------------- +.. autosummary:: + :toctree: generated/ + + plot_njt + njt + biallelic_diplotype_pairwise_distances + +Heterozygosity analysis +----------------------- +.. autosummary:: + :toctree: generated/ + + plot_heterozygosity + roh_hmm + plot_roh + +Diversity analysis +------------------ +.. autosummary:: + :toctree: generated/ + + cohort_diversity_stats + diversity_stats + plot_diversity_stats + +Diplotype clustering +-------------------- +.. autosummary:: + :toctree: generated/ + + plot_diplotype_clustering + plot_diplotype_clustering_advanced + +Fst analysis +------------ +.. autosummary:: + :toctree: generated/ + + average_fst + pairwise_average_fst + plot_pairwise_average_fst + fst_gwss + plot_fst_gwss diff --git a/docs/source/index.rst b/docs/source/index.rst index 98afebed0..773fe9fa9 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -35,6 +35,14 @@ API documentation .. image:: https://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Anopheles_minimus_1.jpg/640px-Anopheles_minimus_1.jpg + .. grid-item-card:: ``Adir1`` + :link: Adir1 + :link-type: doc + + *Anopheles dirus* complex. + + .. image:: https://phil.cdc.gov//PHIL_Images/8777/8777_lores.jpg + Documentation for the `Pf7 `_ (*Plasmodium falciparum*) and `Pv4 `_ (*Plasmodium vivax*) APIs is also available, currently hosted on a separate site. From 53a85e420f14ff3aa17afb5caa58fd9dedeb2eea Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 14 Oct 2025 09:48:54 +1000 Subject: [PATCH 19/41] add updated release path, change from 1.x to 1.0 --- malariagen_data/adir1.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index 00dd3a6e1..b892613c5 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -6,15 +6,13 @@ from .anopheles import AnophelesDataResource MAJOR_VERSION_NUMBER = 1 -MAJOR_VERSION_PATH = "v1.x" -CONFIG_PATH = "v1.x-config.json" +MAJOR_VERSION_PATH = "v1.0" +CONFIG_PATH = "v1.0-config.json" GCS_DEFAULT_URL = "gs://vo_adir_production_us_central1/" -GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_production_us_central1/v1.x/staging" +GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_production_us_central1/release/" GCS_REGION_URLS = { "us-central1": "gs://vo_adir_production_us_central1", } -# XPEHH_GWSS_CACHE_NAME = "adir1_xpehh_gwss_v1" -# IHS_GWSS_CACHE_NAME = "adir1_ihs_gwss_v1" TAXON_PALETTE = px.colors.qualitative.Plotly TAXON_COLORS = { From 0f585919d00d4568c073271f42fdba60450c5550 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 14 Oct 2025 10:08:08 +1000 Subject: [PATCH 20/41] update paths to release directory --- malariagen_data/adir1.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index b892613c5..d1d4fc748 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -8,7 +8,7 @@ MAJOR_VERSION_NUMBER = 1 MAJOR_VERSION_PATH = "v1.0" CONFIG_PATH = "v1.0-config.json" -GCS_DEFAULT_URL = "gs://vo_adir_production_us_central1/" +GCS_DEFAULT_URL = "gs://vo_adir_production_us_central1/release/" GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_production_us_central1/release/" GCS_REGION_URLS = { "us-central1": "gs://vo_adir_production_us_central1", From edee49536488cce2ad57db670952b5d557084935 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 14 Oct 2025 11:02:16 +1000 Subject: [PATCH 21/41] tou added back into sample_metadata --- malariagen_data/anoph/sample_metadata.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index 67145b337..e9a25f252 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -180,16 +180,15 @@ def _parse_general_metadata( axis="columns", ) - # Have commented these out for now as a) this is not a public release and b) for some reason it breaks everything and I haven't had the time to work out why # Add study columns. - # study_info = self.lookup_study_info(sample_set=sample_set) - # for column in study_info: - # df[column] = study_info[column] + study_info = self.lookup_study_info(sample_set=sample_set) + for column in study_info: + df[column] = study_info[column] # Add terms-of-use columns. - # terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) - # for column in terms_of_use_info: - # df[column] = terms_of_use_info[column] + terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) + for column in terms_of_use_info: + df[column] = terms_of_use_info[column] return df From bf5c188c06edd885290b0654ad6788c01f5b96cb Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 14 Oct 2025 11:09:17 +1000 Subject: [PATCH 22/41] corrected path to qc data from sample_metadatax --- malariagen_data/anoph/sample_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index e9a25f252..62baa6870 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -348,7 +348,7 @@ def sequence_qc_metadata( self, sample_sets: Optional[base_params.sample_sets] = None ) -> pd.DataFrame: return self._parse_metadata_paths( - path_template="{release_path}/metadata/general/{sample_set}/sequence_qc_stats.csv", + path_template="{release_path}/metadata/curation/{sample_set}/sequence_qc_stats.csv", parse_metadata_func=self._parse_sequence_qc_metadata, sample_sets=sample_sets, ) From 10e0548c166a9f004f65cdadfd411da25ccfdc28 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 14 Oct 2025 11:10:58 +1000 Subject: [PATCH 23/41] remove pinned ipykernel --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 28d5bdc9b..ca85554c5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -93,7 +93,6 @@ sphinx = "*" pydata-sphinx-theme = "*" sphinx_design = "*" pandas-stubs = "*" -ipykernel = "^6.29.5" [tool.poetry.extras] dev = ["pytest", "pytest-xdist", "pytest-cases", "pytest-cov", "notebook", "jupyterlab", "pre-commit", "ruff", "snakeviz", "mypy", "memory-profiler", "sphinx", "pydata-sphinx-theme", "sphinx_design", "pandas-stubs"] From ad4f661ae2b71347b8df63504d9f5bf0249524a3 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 14 Oct 2025 11:29:14 +1000 Subject: [PATCH 24/41] add initial tests for adir1 --- tests/integration/test_adir1.py | 79 +++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 tests/integration/test_adir1.py diff --git a/tests/integration/test_adir1.py b/tests/integration/test_adir1.py new file mode 100644 index 000000000..5dbd990b3 --- /dev/null +++ b/tests/integration/test_adir1.py @@ -0,0 +1,79 @@ +import numpy as np +import pytest + +from malariagen_data import Adir1, Region +from malariagen_data.util import locate_region, resolve_region + + +def setup_adir1( + url="simplecache::gs://vo_adir_production_us_central1/release/", **kwargs +): + kwargs.setdefault("check_location", False) + kwargs.setdefault("show_progress", False) + if url is None: + # test default URL + # This only tests the setup_af1 default url, not the Af1 default. + # The test_anopheles setup_subclass tests true defaults. + return Adir1(**kwargs) + if url.startswith("simplecache::"): + # configure the directory on the local file system to cache data + kwargs["simplecache"] = dict(cache_storage="gcs_cache") + return Adir1(url, **kwargs) + + +def test_repr(): + adir1 = setup_adir1(check_location=True) + assert isinstance(adir1, Adir1) + r = repr(adir1) + assert isinstance(r, str) + + +@pytest.mark.parametrize( + "region_raw", + [ + "ADIR015707", + "KB672490", + "KB672490:4871446-4871535", + "KB672490:2,630,355-2,633,221", + Region("KB672490", 4871446, 4871535), + ], +) +def test_locate_region(region_raw): + # TODO Migrate this test. + adir1 = setup_adir1() + gene_annotation = adir1.geneset(attributes=["ID"]) + region = resolve_region(adir1, region_raw) + pos = adir1.snp_sites(region=region.contig, field="POS") + ref = adir1.snp_sites(region=region.contig, field="REF") + loc_region = locate_region(region, pos) + + # check types + assert isinstance(loc_region, slice) + assert isinstance(region, Region) + + # check Region with contig + if region_raw == "KB672490": + assert region.contig == "KB672490" + assert region.start is None + assert region.end is None + + # check that Region goes through unchanged + if isinstance(region_raw, Region): + assert region == region_raw + + # check that gene name matches coordinates from the geneset and matches gene sequence + if region_raw == "ADIR015707": + gene = gene_annotation.query("ID == 'ADIR015707'").squeeze() + assert region == Region(gene.contig, gene.start, gene.end) + assert pos[loc_region][0] == gene.start + assert pos[loc_region][-1] == gene.end + assert ( + ref[loc_region][:5].compute() + == np.array(["T", "T", "T", "C", "T"], dtype="S1") + ).all() + + # check string parsing + if region_raw == "KB672490:4871446-4871535": + assert region == Region("KB672490", 4871446, 4871535) + if region_raw == "KB672490:2,630,355-2,633,221": + assert region == Region("KB672490", 2630355, 2633221) From 6f8376caa55a490db258bdb80900da88cf7f9696 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 14 Oct 2025 11:29:14 +1000 Subject: [PATCH 25/41] add initial tests for adir1 --- poetry.lock | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/poetry.lock b/poetry.lock index dd48815c7..1cd2c2516 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. [[package]] name = "accessible-pygments" @@ -397,7 +397,7 @@ description = "Timeout context manager for asyncio programs" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "async_timeout-5.0.1-py3-none-any.whl", hash = "sha256:39e3809566ff85354557ec2398b55e096c8364bacac9405a7a1fa429e77fe76c"}, {file = "async_timeout-5.0.1.tar.gz", hash = "sha256:d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3"}, @@ -921,7 +921,7 @@ description = "Python library for calculating contours of 2D quadrilateral grids optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "contourpy-1.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ba38e3f9f330af820c4b27ceb4b9c7feee5fe0493ea53a8720f4792667465934"}, {file = "contourpy-1.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:dc41ba0714aa2968d1f8674ec97504a8f7e334f48eeacebcaa6256213acb0989"}, @@ -1466,7 +1466,7 @@ description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "exceptiongroup-1.3.0-py3-none-any.whl", hash = "sha256:4d111e6e0c13d0644cad6ddaa7ed0261a0b36971f6d23e7ec9b4b9097da78a10"}, {file = "exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88"}, @@ -2205,7 +2205,7 @@ description = "IPython: Productive Interactive Computing" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "ipython-8.37.0-py3-none-any.whl", hash = "sha256:ed87326596b878932dbcb171e3e698845434d8c61b8d8cd474bf663041a9dcf2"}, {file = "ipython-8.37.0.tar.gz", hash = "sha256:ca815841e1a41a1e6b73a0b08f3038af9b2252564d01fc405356d34033012216"}, @@ -3313,7 +3313,7 @@ description = "Python package for creating and manipulating graphs and networks" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "networkx-3.4.2-py3-none-any.whl", hash = "sha256:df5d4365b724cf81b8c6a7312509d0c22386097011ad1abe274afd5e9d3bbc5f"}, {file = "networkx-3.4.2.tar.gz", hash = "sha256:307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1"}, @@ -3448,7 +3448,7 @@ description = "A Python package providing buffer compression and transformation optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "numcodecs-0.13.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:96add4f783c5ce57cc7e650b6cac79dd101daf887c479a00a29bc1487ced180b"}, {file = "numcodecs-0.13.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:237b7171609e868a20fd313748494444458ccd696062f67e198f7f8f52000c15"}, @@ -5244,7 +5244,7 @@ description = "Fundamental algorithms for scientific computing in Python" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "scipy-1.15.3-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:a345928c86d535060c9c2b25e71e87c39ab2f22fc96e9636bd74d1dbf9de448c"}, {file = "scipy-1.15.3-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:ad3432cb0f9ed87477a8d97f03b763fd1d57709f1bbde3c9369b1dff5503b253"}, @@ -5501,7 +5501,7 @@ description = "Python documentation generator" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version < \"3.11\" and extra == \"dev\"" +markers = "python_version == \"3.10\" and extra == \"dev\"" files = [ {file = "sphinx-8.1.3-py3-none-any.whl", hash = "sha256:09719015511837b76bf6e03e42eb7595ac8c2e41eeb9c29c5b755c6b677992a2"}, {file = "sphinx-8.1.3.tar.gz", hash = "sha256:43c1911eecb0d3e161ad78611bc905d1ad0e523e4ddc202a58a821773dc4c927"}, @@ -5850,7 +5850,7 @@ description = "A lil' TOML parser" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"}, {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"}, @@ -6279,7 +6279,7 @@ description = "N-D labeled arrays and datasets in Python" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "xarray-2025.6.1-py3-none-any.whl", hash = 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"a67f0afbc1c0c640f82de0e96c27f835aa6f9ab6ddb2992b228cf757c5a886f3" From 4c434ae984654664b18ce6f659a88d9b266ffb4e Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 14 Oct 2025 12:34:51 +1000 Subject: [PATCH 26/41] fix broken asset at ref sequence comparison in integration tests --- adir.ipynb | 440 ++++++++++++++++++++++++++++++++ test_release/bin/python | 1 + test_release/bin/python3 | 1 + test_release/bin/python3.10 | 1 + test_release/pyvenv.cfg | 3 + tests/integration/test_adir1.py | 3 +- 6 files changed, 447 insertions(+), 2 deletions(-) create mode 100644 adir.ipynb create mode 120000 test_release/bin/python create mode 120000 test_release/bin/python3 create mode 120000 test_release/bin/python3.10 create mode 100644 test_release/pyvenv.cfg diff --git a/adir.ipynb b/adir.ipynb new file mode 100644 index 000000000..9a9cb0121 --- /dev/null +++ b/adir.ipynb @@ -0,0 +1,440 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "21cfd49f-62d5-4b85-a7b3-ddd6966a1ccd", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import malariagen_data\n", + "import numpy as np\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "2fba0d91-93a8-40fd-8d7b-c55c62645857", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/javascript": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\nconst JS_MIME_TYPE = 'application/javascript';\n const HTML_MIME_TYPE = 'text/html';\n const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n const CLASS_NAME = 'output_bokeh rendered_html';\n\n /**\n * Render data to the DOM node\n */\n function render(props, node) {\n const script = document.createElement(\"script\");\n node.appendChild(script);\n }\n\n 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MalariaGEN Adir1 API client
\n", + " Please note that data are subject to terms of use,\n", + " for more information see \n", + " the MalariaGEN website or contact support@malariagen.net.\n", + " See also the Adir1 API docs.\n", + "
\n", + " Storage URL\n", + " gs://vo_adir_production_us_central1/
\n", + " Data releases available\n", + " 1.x
\n", + " Results cache\n", + " None
\n", + " Cohorts analysis\n", + " 20250710
\n", + " Site filters analysis\n", + " sc_20250610
\n", + " Software version\n", + " malariagen_data 0.0.0
\n", + " Client location\n", + " Queensland, Australia
\n", + " " + ], + "text/plain": [ + "\n", + "Storage URL : gs://vo_adir_production_us_central1/\n", + "Data releases available : 1.x\n", + "Results cache : None\n", + "Cohorts analysis : 20250710\n", + "Site filters analysis : sc_20250610\n", + "Software version : malariagen_data 0.0.0\n", + "Client location : Queensland, Australia\n", + "---\n", + "Please note that data are subject to terms of use,\n", + "for more information see https://www.malariagen.net/data\n", + "or contact support@malariagen.net. For API documentation see \n", + "https://malariagen.github.io/malariagen-data-python/v0.0.0/Adir1.html" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "adir1 = malariagen_data.Adir1()\n", + "adir1" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "ff3e75bb-d04a-40d4-8185-d738ef00ead1", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + } + ], + "source": [ + "df_samples = adir1.sample_metadata()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "ba6a4b73-84ac-46b8-9448-63c49248a16f", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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sample_idderived_sample_idpartner_sample_idcontributorlocationmonthlatitudelongitudesample_setreleasequarter
countryyear
Bangladesh20184747474747474747474747
Cambodia20171212121212121212121212
20181414141414141414141414
20194141414141414141414141
2020207207207207207207207207207207207
Thailand2019219219219219219219219219219219219
\n", + "
" + ], + "text/plain": [ + " sample_id derived_sample_id partner_sample_id contributor \n", + "country year \n", + "Bangladesh 2018 47 47 47 47 \\\n", + "Cambodia 2017 12 12 12 12 \n", + " 2018 14 14 14 14 \n", + " 2019 41 41 41 41 \n", + " 2020 207 207 207 207 \n", + "Thailand 2019 219 219 219 219 \n", + "\n", + " location month latitude longitude sample_set release \n", + "country year \n", + "Bangladesh 2018 47 47 47 47 47 47 \\\n", + "Cambodia 2017 12 12 12 12 12 12 \n", + " 2018 14 14 14 14 14 14 \n", + " 2019 41 41 41 41 41 41 \n", + " 2020 207 207 207 207 207 207 \n", + "Thailand 2019 219 219 219 219 219 219 \n", + "\n", + " quarter \n", + "country year \n", + "Bangladesh 2018 47 \n", + "Cambodia 2017 12 \n", + " 2018 14 \n", + " 2019 41 \n", + " 2020 207 \n", + "Thailand 2019 219 " + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df_samples.groupby(['country','year']).count()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "60556bb1-9469-45d6-a96e-73e1d542e0fb", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Compute SNP allele counts: 0%| | 0/780 [00:00 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m100000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msite_mask\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mdirus\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:136\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 131\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_metadata(\n\u001b[1;32m 132\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39msample_sets,\n\u001b[1;32m 133\u001b[0m )\n\u001b[1;32m 135\u001b[0m \u001b[38;5;66;03m# Ensure aligned with genotype data.\u001b[39;00m\n\u001b[0;32m--> 136\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[43mdf_samples\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mset_index\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43msample_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloc\u001b[49m\u001b[43m[\u001b[49m\u001b[43msamples\u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mreset_index()\n\u001b[1;32m 138\u001b[0m \u001b[38;5;66;03m# Combine coords and sample metadata.\u001b[39;00m\n\u001b[1;32m 139\u001b[0m df_coords \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame(\n\u001b[1;32m 140\u001b[0m {\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mPC\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mi\u001b[38;5;250m \u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;250m \u001b[39m\u001b[38;5;241m1\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m: coords[:, i] \u001b[38;5;28;01mfor\u001b[39;00m i \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mrange\u001b[39m(coords\u001b[38;5;241m.\u001b[39mshape[\u001b[38;5;241m1\u001b[39m])}\n\u001b[1;32m 141\u001b[0m )\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexing.py:1103\u001b[0m, in \u001b[0;36m_LocationIndexer.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 1100\u001b[0m axis \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39maxis \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;241m0\u001b[39m\n\u001b[1;32m 1102\u001b[0m maybe_callable \u001b[38;5;241m=\u001b[39m com\u001b[38;5;241m.\u001b[39mapply_if_callable(key, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobj)\n\u001b[0;32m-> 1103\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_getitem_axis\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmaybe_callable\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maxis\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexing.py:1332\u001b[0m, in \u001b[0;36m_LocIndexer._getitem_axis\u001b[0;34m(self, key, axis)\u001b[0m\n\u001b[1;32m 1329\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(key, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mndim\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;129;01mand\u001b[39;00m key\u001b[38;5;241m.\u001b[39mndim \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m 1330\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCannot index with multidimensional key\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m-> 1332\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_getitem_iterable\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maxis\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1334\u001b[0m \u001b[38;5;66;03m# nested tuple slicing\u001b[39;00m\n\u001b[1;32m 1335\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_nested_tuple(key, labels):\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexing.py:1272\u001b[0m, in \u001b[0;36m_LocIndexer._getitem_iterable\u001b[0;34m(self, key, axis)\u001b[0m\n\u001b[1;32m 1269\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_validate_key(key, axis)\n\u001b[1;32m 1271\u001b[0m \u001b[38;5;66;03m# A collection of keys\u001b[39;00m\n\u001b[0;32m-> 1272\u001b[0m keyarr, indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_listlike_indexer\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1273\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobj\u001b[38;5;241m.\u001b[39m_reindex_with_indexers(\n\u001b[1;32m 1274\u001b[0m {axis: [keyarr, indexer]}, copy\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, allow_dups\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m 1275\u001b[0m )\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexing.py:1462\u001b[0m, in \u001b[0;36m_LocIndexer._get_listlike_indexer\u001b[0;34m(self, key, axis)\u001b[0m\n\u001b[1;32m 1459\u001b[0m ax \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobj\u001b[38;5;241m.\u001b[39m_get_axis(axis)\n\u001b[1;32m 1460\u001b[0m axis_name \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobj\u001b[38;5;241m.\u001b[39m_get_axis_name(axis)\n\u001b[0;32m-> 1462\u001b[0m keyarr, indexer \u001b[38;5;241m=\u001b[39m \u001b[43max\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1464\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m keyarr, indexer\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5938\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[0;32m-> 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "\u001b[0;31mKeyError\u001b[0m: \"['VBS45975-6296STDY1024453', 'VBS45982-6296STDY9478589', 'VBS45983-6296STDY1024453', 'VBS45984-6296STDY1024453', 'VBS45985-6296STDY1024453', 'VBS45986-6296STDY1024454', 'VBS45987-6296STDY1024454', 'VBS45988-6296STDY1024454', 'VBS45989-6296STDY1024454', 'VBS45991-6296STDY1024454', 'VBS45992-6296STDY1024454', 'VBS45993-6296STDY1024454', 'VBS45994-6296STDY1024454', 'VBS45995-6296STDY1024454', 'VBS45996-6296STDY1024455', 'VBS45997-6296STDY1024455', 'VBS45998-6296STDY1024455', 'VBS45999-6296STDY1024455', 'VBS46000-6296STDY1024455', 'VBS46001-6296STDY1024455', 'VBS46002-6296STDY1024455', 'VBS46003-6296STDY1024455', 'VBS46004-6296STDY1024455', 'VBS46006-6296STDY1024456', 'VBS46007-6296STDY1024456', 'VBS46008-6296STDY1024456', 'VBS46009-6296STDY1024456', 'VBS46010-6296STDY1024456', 'VBS46011-6296STDY1024456', 'VBS46012-6296STDY1024456', 'VBS46013-6296STDY1024456', 'VBS46014-6296STDY1024456', 'VBS46016-6296STDY1024457', 'VBS46017-6296STDY1024457', 'VBS46019-6296STDY1024457', 'VBS46020-6296STDY1024457', 'VBS46021-6296STDY1024457', 'VBS46022-6296STDY1024457', 'VBS46025-6296STDY1024457', 'VBS46026-6296STDY1024458', 'VBS46027-6296STDY1024458', 'VBS46028-6296STDY1024458', 'VBS46029-6296STDY1024458', 'VBS46030-6296STDY1024458', 'VBS46031-6296STDY1024458', 'VBS46032-6296STDY1024458', 'VBS46033-6296STDY1024458', 'VBS46034-6296STDY1024458', 'VBS46035-6296STDY1024458', 'VBS46036-6296STDY1024459', 'VBS46037-6296STDY1024459', 'VBS46038-6296STDY1024459', 'VBS46039-6296STDY1024459', 'VBS46040-6296STDY1024459', 'VBS46041-6296STDY1024459', 'VBS46043-6296STDY1024459', 'VBS46044-6296STDY1024459', 'VBS46045-6296STDY1024459', 'VBS46046-6296STDY1024460', 'VBS46047-6296STDY1024460', 'VBS46048-6296STDY1024460', 'VBS46049-6296STDY1024460', 'VBS46051-6296STDY1024460', 'VBS46052-6296STDY1024460', 'VBS46053-6296STDY1024460', 'VBS46054-6296STDY1024460', 'VBS46055-6296STDY1024460', 'VBS46056-6296STDY1024461', 'VBS46057-6296STDY1024461', 'VBS46060-6296STDY1024461', 'VBS46061-6296STDY1024461', 'VBS46063-6296STDY1024461', 'VBS46064-6296STDY1024461', 'VBS46065-6296STDY1024461', 'VBS46068-6296STDY1024462', 'VBS46069-6296STDY1024462', 'VBS46070-6296STDY1024462', 'VBS46071-6296STDY1024462', 'VBS46072-6296STDY1024462', 'VBS46073-6296STDY1024462', 'VBS46074-6296STDY1024463', 'VBS46075-6296STDY1024463', 'VBS46076-6296STDY1024463', 'VBS46077-6296STDY1024463', 'VBS46079-6296STDY1024463', 'VBS46080-6296STDY1024463', 'VBS46081-6296STDY1024463', 'VBS46082-6296STDY1024463', 'VBS46085-6296STDY1024464', 'VBS46086-6296STDY1024464', 'VBS46089-6296STDY1024464', 'VBS46090-6296STDY1024464', 'VBS46091-6296STDY1024464', 'VBS46092-6296STDY1024464', 'VBS46093-6296STDY1024464', 'VBS46094-6296STDY1024465', 'VBS46095-6296STDY1024465', 'VBS46096-6296STDY1024465', 'VBS46097-6296STDY1024465', 'VBS46099-6296STDY1024465', 'VBS46100-6296STDY1024465', 'VBS46101-6296STDY1024465', 'VBS46102-6296STDY1024465', 'VBS46103-6296STDY1024465', 'VBS46104-6296STDY1024466', 'VBS46105-6296STDY1024466', 'VBS46106-6296STDY1024466', 'VBS46107-6296STDY1024466', 'VBS46108-6296STDY1024466', 'VBS46109-6296STDY1024466', 'VBS46110-6296STDY1024466', 'VBS46111-6296STDY1024466', 'VBS46112-6296STDY1024466', 'VBS46113-6296STDY1024466', 'VBS46114-6296STDY1024467', 'VBS46115-6296STDY1024467', 'VBS46116-6296STDY1024467', 'VBS46117-6296STDY1024467', 'VBS46118-6296STDY1024467', 'VBS46119-6296STDY1024467', 'VBS46120-6296STDY1024467', 'VBS46122-6296STDY1024467', 'VBS46123-6296STDY1024467', 'VBS46124-6296STDY1024468', 'VBS46125-6296STDY1024468', 'VBS46126-6296STDY1024468', 'VBS46127-6296STDY1024468', 'VBS46128-6296STDY1024468', 'VBS46129-6296STDY1024468', 'VBS46130-6296STDY1024468', 'VBS46131-6296STDY1024468', 'VBS46132-6296STDY1024468', 'VBS46133-6296STDY1024468', 'VBS46134-6296STDY1024469', 'VBS46135-6296STDY1024469', 'VBS46136-6296STDY1024469', 'VBS46137-6296STDY1024469', 'VBS46138-6296STDY1024469', 'VBS46139-6296STDY1024469', 'VBS46140-6296STDY1024469', 'VBS46142-6296STDY1024469', 'VBS46143-6296STDY1024469', 'VBS46144-6296STDY1024470', 'VBS46147-6296STDY1024470', 'VBS46148-6296STDY1024470', 'VBS46149-6296STDY1024470', 'VBS46150-6296STDY1024470', 'VBS46151-6296STDY1024470', 'VBS46152-6296STDY1024470', 'VBS46153-6296STDY1024470', 'VBS46155-6296STDY1024471', 'VBS46156-6296STDY1024471', 'VBS46157-6296STDY1024471', 'VBS46158-6296STDY1024471', 'VBS46160-6296STDY1024471', 'VBS46161-6296STDY1024471', 'VBS46162-6296STDY1024471', 'VBS46163-6296STDY1024472', 'VBS46164-6296STDY1024472', 'VBS46165-6296STDY1024472', 'VBS46166-6296STDY1024472', 'VBS46170-6296STDY1024472', 'VBS46171-6296STDY1024472', 'VBS46174-6296STDY1024473', 'VBS46176-6296STDY1024473', 'VBS46177-6296STDY1024473', 'VBS46178-6296STDY1024473', 'VBS46179-6296STDY1024473', 'VBS46181-6296STDY1024473', 'VBS46182-6296STDY1024473', 'VBS46184-6296STDY1024474', 'VBS46185-6296STDY1024474', 'VBS46186-6296STDY1024474', 'VBS46193-6296STDY1024474', 'VBS46194-6296STDY1024475', 'VBS46195-6296STDY1024475', 'VBS46196-6296STDY1024475', 'VBS46197-6296STDY1024475', 'VBS46199-6296STDY1024475', 'VBS46200-6296STDY1024475', 'VBS46201-6296STDY1024475', 'VBS46202-6296STDY1024475', 'VBS46203-6296STDY1024475', 'VBS46204-6296STDY1024476', 'VBS46205-6296STDY1024476', 'VBS46206-6296STDY1024476', 'VBS46207-6296STDY1024476'] not in index\"" + ] + } + ], + "source": [ + "pca = adir1.pca(region = \"KB672868\", n_snps=100000, sample_query = \"country == 'Thailand'\", site_mask = \"dirus\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d1b167fd-06e8-40b8-ba5f-5e8fa43dc931", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "malariagen-data-py3.10 (3.10.10)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/test_release/bin/python b/test_release/bin/python new file mode 120000 index 000000000..a9cc0f749 --- /dev/null +++ b/test_release/bin/python @@ -0,0 +1 @@ +/Users/dennistpw/miniconda3/bin/python \ No newline at end of file diff --git a/test_release/bin/python3 b/test_release/bin/python3 new file mode 120000 index 000000000..d8654aa0e --- /dev/null +++ b/test_release/bin/python3 @@ -0,0 +1 @@ +python \ No newline at end of file diff --git a/test_release/bin/python3.10 b/test_release/bin/python3.10 new file mode 120000 index 000000000..d8654aa0e --- /dev/null +++ b/test_release/bin/python3.10 @@ -0,0 +1 @@ +python \ No newline at end of file diff --git a/test_release/pyvenv.cfg b/test_release/pyvenv.cfg new file mode 100644 index 000000000..169b295f8 --- /dev/null +++ b/test_release/pyvenv.cfg @@ -0,0 +1,3 @@ +home = /Users/dennistpw/miniconda3/bin +include-system-site-packages = false +version = 3.10.10 diff --git a/tests/integration/test_adir1.py b/tests/integration/test_adir1.py index 5dbd990b3..8d8de9816 100644 --- a/tests/integration/test_adir1.py +++ b/tests/integration/test_adir1.py @@ -68,8 +68,7 @@ def test_locate_region(region_raw): assert pos[loc_region][0] == gene.start assert pos[loc_region][-1] == gene.end assert ( - ref[loc_region][:5].compute() - == np.array(["T", "T", "T", "C", "T"], dtype="S1") + ref[loc_region][:5].compute() == np.array(["T", "T", "G", "T", "T"]) ).all() # check string parsing From 0f7aa4db73577fa47d9b703e85f64471c83d2f7f Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 14 Oct 2025 12:36:29 +1000 Subject: [PATCH 27/41] tidy --- adir.ipynb | 440 ------------------------------------ test_release/bin/python | 1 - test_release/bin/python3 | 1 - test_release/bin/python3.10 | 1 - test_release/pyvenv.cfg | 3 - 5 files changed, 446 deletions(-) delete mode 100644 adir.ipynb delete mode 120000 test_release/bin/python delete mode 120000 test_release/bin/python3 delete mode 120000 test_release/bin/python3.10 delete mode 100644 test_release/pyvenv.cfg diff --git a/adir.ipynb b/adir.ipynb deleted file mode 100644 index 9a9cb0121..000000000 --- a/adir.ipynb +++ /dev/null @@ -1,440 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "21cfd49f-62d5-4b85-a7b3-ddd6966a1ccd", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import malariagen_data\n", - "import numpy as np\n" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "2fba0d91-93a8-40fd-8d7b-c55c62645857", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "application/javascript": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\nconst JS_MIME_TYPE = 'application/javascript';\n const HTML_MIME_TYPE = 'text/html';\n const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n const CLASS_NAME = 'output_bokeh rendered_html';\n\n /**\n * Render data to the DOM node\n */\n function render(props, node) {\n const script = document.createElement(\"script\");\n node.appendChild(script);\n }\n\n /**\n * Handle when an output is cleared or removed\n */\n function handleClearOutput(event, handle) {\n function drop(id) {\n const view = Bokeh.index.get_by_id(id)\n if (view != null) {\n view.model.document.clear()\n Bokeh.index.delete(view)\n }\n }\n\n const cell = handle.cell;\n\n const id = cell.output_area._bokeh_element_id;\n const server_id = cell.output_area._bokeh_server_id;\n\n // Clean up Bokeh references\n if (id != null) {\n drop(id)\n }\n\n if (server_id !== undefined) {\n // Clean up Bokeh references\n const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n cell.notebook.kernel.execute(cmd_clean, {\n iopub: {\n output: function(msg) {\n const id = msg.content.text.trim()\n drop(id)\n }\n }\n });\n // Destroy server and session\n const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n cell.notebook.kernel.execute(cmd_destroy);\n }\n }\n\n /**\n * Handle when a new output is added\n */\n function handleAddOutput(event, handle) {\n const output_area = handle.output_area;\n const output = handle.output;\n\n // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n if ((output.output_type != \"display_data\") || 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\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
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\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
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MalariaGEN Adir1 API client
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sample_idderived_sample_idpartner_sample_idcontributorlocationmonthlatitudelongitudesample_setreleasequarter
countryyear
Bangladesh20184747474747474747474747
Cambodia20171212121212121212121212
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\n", - "
" - ], - "text/plain": [ - " sample_id derived_sample_id partner_sample_id contributor \n", - "country year \n", - "Bangladesh 2018 47 47 47 47 \\\n", - "Cambodia 2017 12 12 12 12 \n", - " 2018 14 14 14 14 \n", - " 2019 41 41 41 41 \n", - " 2020 207 207 207 207 \n", - "Thailand 2019 219 219 219 219 \n", - "\n", - " location month latitude longitude sample_set release \n", - "country year \n", - "Bangladesh 2018 47 47 47 47 47 47 \\\n", - "Cambodia 2017 12 12 12 12 12 12 \n", - " 2018 14 14 14 14 14 14 \n", - " 2019 41 41 41 41 41 41 \n", - " 2020 207 207 207 207 207 207 \n", - "Thailand 2019 219 219 219 219 219 219 \n", - "\n", - " quarter \n", - "country year \n", - "Bangladesh 2018 47 \n", - "Cambodia 2017 12 \n", - " 2018 14 \n", - " 2019 41 \n", - " 2020 207 \n", - "Thailand 2019 219 " - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df_samples.groupby(['country','year']).count()" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "60556bb1-9469-45d6-a96e-73e1d542e0fb", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " \r" - ] - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "Compute SNP allele counts: 0%| | 0/780 [00:00 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m100000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msite_mask\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mdirus\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:136\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 131\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_metadata(\n\u001b[1;32m 132\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39msample_sets,\n\u001b[1;32m 133\u001b[0m )\n\u001b[1;32m 135\u001b[0m \u001b[38;5;66;03m# Ensure aligned with genotype data.\u001b[39;00m\n\u001b[0;32m--> 136\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[43mdf_samples\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mset_index\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43msample_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloc\u001b[49m\u001b[43m[\u001b[49m\u001b[43msamples\u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mreset_index()\n\u001b[1;32m 138\u001b[0m \u001b[38;5;66;03m# Combine coords and sample metadata.\u001b[39;00m\n\u001b[1;32m 139\u001b[0m df_coords \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame(\n\u001b[1;32m 140\u001b[0m {\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mPC\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mi\u001b[38;5;250m \u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;250m \u001b[39m\u001b[38;5;241m1\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m: coords[:, i] \u001b[38;5;28;01mfor\u001b[39;00m i \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mrange\u001b[39m(coords\u001b[38;5;241m.\u001b[39mshape[\u001b[38;5;241m1\u001b[39m])}\n\u001b[1;32m 141\u001b[0m )\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexing.py:1103\u001b[0m, in \u001b[0;36m_LocationIndexer.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 1100\u001b[0m axis \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39maxis \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;241m0\u001b[39m\n\u001b[1;32m 1102\u001b[0m maybe_callable \u001b[38;5;241m=\u001b[39m com\u001b[38;5;241m.\u001b[39mapply_if_callable(key, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobj)\n\u001b[0;32m-> 1103\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_getitem_axis\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmaybe_callable\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maxis\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexing.py:1332\u001b[0m, in \u001b[0;36m_LocIndexer._getitem_axis\u001b[0;34m(self, key, axis)\u001b[0m\n\u001b[1;32m 1329\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(key, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mndim\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;129;01mand\u001b[39;00m key\u001b[38;5;241m.\u001b[39mndim \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m 1330\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCannot index with multidimensional key\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m-> 1332\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_getitem_iterable\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maxis\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1334\u001b[0m \u001b[38;5;66;03m# nested tuple slicing\u001b[39;00m\n\u001b[1;32m 1335\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_nested_tuple(key, labels):\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexing.py:1272\u001b[0m, in \u001b[0;36m_LocIndexer._getitem_iterable\u001b[0;34m(self, key, axis)\u001b[0m\n\u001b[1;32m 1269\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_validate_key(key, axis)\n\u001b[1;32m 1271\u001b[0m \u001b[38;5;66;03m# A collection of keys\u001b[39;00m\n\u001b[0;32m-> 1272\u001b[0m keyarr, indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_listlike_indexer\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1273\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobj\u001b[38;5;241m.\u001b[39m_reindex_with_indexers(\n\u001b[1;32m 1274\u001b[0m {axis: [keyarr, indexer]}, copy\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, allow_dups\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m 1275\u001b[0m )\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexing.py:1462\u001b[0m, in \u001b[0;36m_LocIndexer._get_listlike_indexer\u001b[0;34m(self, key, axis)\u001b[0m\n\u001b[1;32m 1459\u001b[0m ax \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobj\u001b[38;5;241m.\u001b[39m_get_axis(axis)\n\u001b[1;32m 1460\u001b[0m axis_name \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobj\u001b[38;5;241m.\u001b[39m_get_axis_name(axis)\n\u001b[0;32m-> 1462\u001b[0m keyarr, indexer \u001b[38;5;241m=\u001b[39m \u001b[43max\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1464\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m keyarr, indexer\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5938\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[0;32m-> 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", - "\u001b[0;31mKeyError\u001b[0m: \"['VBS45975-6296STDY1024453', 'VBS45982-6296STDY9478589', 'VBS45983-6296STDY1024453', 'VBS45984-6296STDY1024453', 'VBS45985-6296STDY1024453', 'VBS45986-6296STDY1024454', 'VBS45987-6296STDY1024454', 'VBS45988-6296STDY1024454', 'VBS45989-6296STDY1024454', 'VBS45991-6296STDY1024454', 'VBS45992-6296STDY1024454', 'VBS45993-6296STDY1024454', 'VBS45994-6296STDY1024454', 'VBS45995-6296STDY1024454', 'VBS45996-6296STDY1024455', 'VBS45997-6296STDY1024455', 'VBS45998-6296STDY1024455', 'VBS45999-6296STDY1024455', 'VBS46000-6296STDY1024455', 'VBS46001-6296STDY1024455', 'VBS46002-6296STDY1024455', 'VBS46003-6296STDY1024455', 'VBS46004-6296STDY1024455', 'VBS46006-6296STDY1024456', 'VBS46007-6296STDY1024456', 'VBS46008-6296STDY1024456', 'VBS46009-6296STDY1024456', 'VBS46010-6296STDY1024456', 'VBS46011-6296STDY1024456', 'VBS46012-6296STDY1024456', 'VBS46013-6296STDY1024456', 'VBS46014-6296STDY1024456', 'VBS46016-6296STDY1024457', 'VBS46017-6296STDY1024457', 'VBS46019-6296STDY1024457', 'VBS46020-6296STDY1024457', 'VBS46021-6296STDY1024457', 'VBS46022-6296STDY1024457', 'VBS46025-6296STDY1024457', 'VBS46026-6296STDY1024458', 'VBS46027-6296STDY1024458', 'VBS46028-6296STDY1024458', 'VBS46029-6296STDY1024458', 'VBS46030-6296STDY1024458', 'VBS46031-6296STDY1024458', 'VBS46032-6296STDY1024458', 'VBS46033-6296STDY1024458', 'VBS46034-6296STDY1024458', 'VBS46035-6296STDY1024458', 'VBS46036-6296STDY1024459', 'VBS46037-6296STDY1024459', 'VBS46038-6296STDY1024459', 'VBS46039-6296STDY1024459', 'VBS46040-6296STDY1024459', 'VBS46041-6296STDY1024459', 'VBS46043-6296STDY1024459', 'VBS46044-6296STDY1024459', 'VBS46045-6296STDY1024459', 'VBS46046-6296STDY1024460', 'VBS46047-6296STDY1024460', 'VBS46048-6296STDY1024460', 'VBS46049-6296STDY1024460', 'VBS46051-6296STDY1024460', 'VBS46052-6296STDY1024460', 'VBS46053-6296STDY1024460', 'VBS46054-6296STDY1024460', 'VBS46055-6296STDY1024460', 'VBS46056-6296STDY1024461', 'VBS46057-6296STDY1024461', 'VBS46060-6296STDY1024461', 'VBS46061-6296STDY1024461', 'VBS46063-6296STDY1024461', 'VBS46064-6296STDY1024461', 'VBS46065-6296STDY1024461', 'VBS46068-6296STDY1024462', 'VBS46069-6296STDY1024462', 'VBS46070-6296STDY1024462', 'VBS46071-6296STDY1024462', 'VBS46072-6296STDY1024462', 'VBS46073-6296STDY1024462', 'VBS46074-6296STDY1024463', 'VBS46075-6296STDY1024463', 'VBS46076-6296STDY1024463', 'VBS46077-6296STDY1024463', 'VBS46079-6296STDY1024463', 'VBS46080-6296STDY1024463', 'VBS46081-6296STDY1024463', 'VBS46082-6296STDY1024463', 'VBS46085-6296STDY1024464', 'VBS46086-6296STDY1024464', 'VBS46089-6296STDY1024464', 'VBS46090-6296STDY1024464', 'VBS46091-6296STDY1024464', 'VBS46092-6296STDY1024464', 'VBS46093-6296STDY1024464', 'VBS46094-6296STDY1024465', 'VBS46095-6296STDY1024465', 'VBS46096-6296STDY1024465', 'VBS46097-6296STDY1024465', 'VBS46099-6296STDY1024465', 'VBS46100-6296STDY1024465', 'VBS46101-6296STDY1024465', 'VBS46102-6296STDY1024465', 'VBS46103-6296STDY1024465', 'VBS46104-6296STDY1024466', 'VBS46105-6296STDY1024466', 'VBS46106-6296STDY1024466', 'VBS46107-6296STDY1024466', 'VBS46108-6296STDY1024466', 'VBS46109-6296STDY1024466', 'VBS46110-6296STDY1024466', 'VBS46111-6296STDY1024466', 'VBS46112-6296STDY1024466', 'VBS46113-6296STDY1024466', 'VBS46114-6296STDY1024467', 'VBS46115-6296STDY1024467', 'VBS46116-6296STDY1024467', 'VBS46117-6296STDY1024467', 'VBS46118-6296STDY1024467', 'VBS46119-6296STDY1024467', 'VBS46120-6296STDY1024467', 'VBS46122-6296STDY1024467', 'VBS46123-6296STDY1024467', 'VBS46124-6296STDY1024468', 'VBS46125-6296STDY1024468', 'VBS46126-6296STDY1024468', 'VBS46127-6296STDY1024468', 'VBS46128-6296STDY1024468', 'VBS46129-6296STDY1024468', 'VBS46130-6296STDY1024468', 'VBS46131-6296STDY1024468', 'VBS46132-6296STDY1024468', 'VBS46133-6296STDY1024468', 'VBS46134-6296STDY1024469', 'VBS46135-6296STDY1024469', 'VBS46136-6296STDY1024469', 'VBS46137-6296STDY1024469', 'VBS46138-6296STDY1024469', 'VBS46139-6296STDY1024469', 'VBS46140-6296STDY1024469', 'VBS46142-6296STDY1024469', 'VBS46143-6296STDY1024469', 'VBS46144-6296STDY1024470', 'VBS46147-6296STDY1024470', 'VBS46148-6296STDY1024470', 'VBS46149-6296STDY1024470', 'VBS46150-6296STDY1024470', 'VBS46151-6296STDY1024470', 'VBS46152-6296STDY1024470', 'VBS46153-6296STDY1024470', 'VBS46155-6296STDY1024471', 'VBS46156-6296STDY1024471', 'VBS46157-6296STDY1024471', 'VBS46158-6296STDY1024471', 'VBS46160-6296STDY1024471', 'VBS46161-6296STDY1024471', 'VBS46162-6296STDY1024471', 'VBS46163-6296STDY1024472', 'VBS46164-6296STDY1024472', 'VBS46165-6296STDY1024472', 'VBS46166-6296STDY1024472', 'VBS46170-6296STDY1024472', 'VBS46171-6296STDY1024472', 'VBS46174-6296STDY1024473', 'VBS46176-6296STDY1024473', 'VBS46177-6296STDY1024473', 'VBS46178-6296STDY1024473', 'VBS46179-6296STDY1024473', 'VBS46181-6296STDY1024473', 'VBS46182-6296STDY1024473', 'VBS46184-6296STDY1024474', 'VBS46185-6296STDY1024474', 'VBS46186-6296STDY1024474', 'VBS46193-6296STDY1024474', 'VBS46194-6296STDY1024475', 'VBS46195-6296STDY1024475', 'VBS46196-6296STDY1024475', 'VBS46197-6296STDY1024475', 'VBS46199-6296STDY1024475', 'VBS46200-6296STDY1024475', 'VBS46201-6296STDY1024475', 'VBS46202-6296STDY1024475', 'VBS46203-6296STDY1024475', 'VBS46204-6296STDY1024476', 'VBS46205-6296STDY1024476', 'VBS46206-6296STDY1024476', 'VBS46207-6296STDY1024476'] not in index\"" - ] - } - ], - "source": [ - "pca = adir1.pca(region = \"KB672868\", n_snps=100000, sample_query = \"country == 'Thailand'\", site_mask = \"dirus\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "d1b167fd-06e8-40b8-ba5f-5e8fa43dc931", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "malariagen-data-py3.10 (3.10.10)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/test_release/bin/python b/test_release/bin/python deleted file mode 120000 index a9cc0f749..000000000 --- a/test_release/bin/python +++ /dev/null @@ -1 +0,0 @@ -/Users/dennistpw/miniconda3/bin/python \ No newline at end of file diff --git a/test_release/bin/python3 b/test_release/bin/python3 deleted file mode 120000 index d8654aa0e..000000000 --- a/test_release/bin/python3 +++ /dev/null @@ -1 +0,0 @@ -python \ No newline at end of file diff --git a/test_release/bin/python3.10 b/test_release/bin/python3.10 deleted file mode 120000 index d8654aa0e..000000000 --- a/test_release/bin/python3.10 +++ /dev/null @@ -1 +0,0 @@ -python \ No newline at end of file diff --git a/test_release/pyvenv.cfg b/test_release/pyvenv.cfg deleted file mode 100644 index 169b295f8..000000000 --- a/test_release/pyvenv.cfg +++ /dev/null @@ -1,3 +0,0 @@ -home = /Users/dennistpw/miniconda3/bin -include-system-site-packages = false -version = 3.10.10 From 844eebea46b6ee80c74b6c4f35c552c7a3e04ad9 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Wed, 15 Oct 2025 10:37:47 +1000 Subject: [PATCH 28/41] Change location to release bucket --- malariagen_data/adir1.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index d1d4fc748..7abdecbbe 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -8,10 +8,10 @@ MAJOR_VERSION_NUMBER = 1 MAJOR_VERSION_PATH = "v1.0" CONFIG_PATH = "v1.0-config.json" -GCS_DEFAULT_URL = "gs://vo_adir_production_us_central1/release/" -GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_production_us_central1/release/" +GCS_DEFAULT_URL = "gs://vo_adir_release_us_central1/" +GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_release_us_central1/" GCS_REGION_URLS = { - "us-central1": "gs://vo_adir_production_us_central1", + "us-central1": "gs://vo_adir_release_us_central1", } TAXON_PALETTE = px.colors.qualitative.Plotly From 27560f4489fc29339fccbbcb96b4054f36347bf1 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Sun, 19 Oct 2025 13:57:57 +1000 Subject: [PATCH 29/41] update bucket path in class file --- malariagen_data/adir1.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index 7abdecbbe..e2902b430 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -60,7 +60,7 @@ class Adir1(AnophelesDataResource): in a directory named "gcs_cache": >>> adir1 = malariagen_data.Adir1( - ... "simplecache::gs://vo_adir_production_us_central1", + ... "simplecache::gs://vo_adir_release_us_central1", ... simplecache=dict(cache_storage="gcs_cache"), ... ) From 108ce5552ce29bf01cee76c089e8f5aec24f4a4d Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 21 Oct 2025 10:38:31 +1000 Subject: [PATCH 30/41] add new bucket path --- malariagen_data/adir1.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index e2902b430..d5e1e7134 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -8,10 +8,10 @@ MAJOR_VERSION_NUMBER = 1 MAJOR_VERSION_PATH = "v1.0" CONFIG_PATH = "v1.0-config.json" -GCS_DEFAULT_URL = "gs://vo_adir_release_us_central1/" -GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_release_us_central1/" +GCS_DEFAULT_URL = "gs://vo_adir_release_master_us_central1/" +GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_release_master_us_central1/" GCS_REGION_URLS = { - "us-central1": "gs://vo_adir_release_us_central1", + "us-central1": "gs://vo_adir_release_master_us_central1", } TAXON_PALETTE = px.colors.qualitative.Plotly @@ -60,7 +60,7 @@ class Adir1(AnophelesDataResource): in a directory named "gcs_cache": >>> adir1 = malariagen_data.Adir1( - ... "simplecache::gs://vo_adir_release_us_central1", + ... "simplecache::gs://vo_adir_release_master_us_central1", ... simplecache=dict(cache_storage="gcs_cache"), ... ) From ccba40215caaf2eeee4565f912565d13a37e8b8e Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Wed, 22 Oct 2025 08:02:46 +1000 Subject: [PATCH 31/41] ud bucket location in adir1 integration test --- tests/integration/test_adir1.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/tests/integration/test_adir1.py b/tests/integration/test_adir1.py index 8d8de9816..1952d0ccd 100644 --- a/tests/integration/test_adir1.py +++ b/tests/integration/test_adir1.py @@ -5,9 +5,7 @@ from malariagen_data.util import locate_region, resolve_region -def setup_adir1( - url="simplecache::gs://vo_adir_production_us_central1/release/", **kwargs -): +def setup_adir1(url="simplecache::gs://vo_adir_release_master_us_central1/", **kwargs): kwargs.setdefault("check_location", False) kwargs.setdefault("show_progress", False) if url is None: From ef780312c8790a3f95c5a4983bc77e26f3e4a8ee Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Wed, 29 Oct 2025 16:26:27 +1000 Subject: [PATCH 32/41] force sync adir1.x with local --- malariagen_data/adir1.py | 3 --- malariagen_data/anopheles.py | 7 ++++++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index d5e1e7134..5b2f28799 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -71,9 +71,6 @@ class Adir1(AnophelesDataResource): """ - # _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME - # _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME - def __init__( self, url=None, diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py index 3c8572b67..2da2e5735 100644 --- a/malariagen_data/anopheles.py +++ b/malariagen_data/anopheles.py @@ -556,6 +556,11 @@ def _sample_count_het( return sample_id, sample_set, windows, counts + @property + @abstractmethod + def _roh_hmm_cache_name(self): + raise NotImplementedError("Must override _roh_hmm_cache_name") + @check_types @doc( summary="Infer runs of homozygosity for a single sample over a genome region.", @@ -577,7 +582,7 @@ def roh_hmm( resolved_region: Region = parse_single_region(self, region) - name = "roh" + name = self._roh_hmm_cache_name params = dict( sample=sample, From 686a5560761b567bf89cee4b6775dca089d49c02 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Thu, 30 Oct 2025 13:48:03 +1000 Subject: [PATCH 33/41] add conf tests for dirus, simulated data, fixture, etc --- tests/anoph/conftest.py | 325 ++++++++++++++++++ .../samples.admin_units.csv | 48 +++ .../samples.cohorts.csv | 48 +++ .../1276-AD-BD-ALAM-VMF00156/samples.taxa.csv | 48 +++ .../samples.admin_units.csv | 27 ++ .../samples.cohorts.csv | 27 ++ .../samples.taxa.csv | 27 ++ .../sequence_qc_stats.csv | 48 +++ .../sequence_qc_stats.csv | 27 ++ .../1276-AD-BD-ALAM-VMF00156/samples.meta.csv | 48 +++ .../sequence_qc_stats.csv | 48 +++ .../1276-AD-BD-ALAM-VMF00156/wgs_snp_data.csv | 48 +++ .../samples.meta.csv | 27 ++ .../sequence_qc_stats.csv | 27 ++ .../wgs_snp_data.csv | 27 ++ tests/anoph/test_sample_metadata.py | 36 ++ tests/anoph/test_snp_data.py | 23 ++ 17 files changed, 909 insertions(+) create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.admin_units.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.cohorts.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.taxa.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.admin_units.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.cohorts.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.taxa.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/samples.meta.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_snp_data.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/samples.meta.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_snp_data.csv diff --git a/tests/anoph/conftest.py b/tests/anoph/conftest.py index 9f258c295..7e7cd94d5 100644 --- a/tests/anoph/conftest.py +++ b/tests/anoph/conftest.py @@ -2364,6 +2364,326 @@ def init_cnv_discordant_read_calls(self): ) +class Adir1Simulator(AnophelesSimulator): + def __init__(self, fixture_dir): + super().__init__( + fixture_dir=fixture_dir, + bucket="vo_adir_release_master_us_central1", + releases=("1.0",), + has_aims=False, + has_cohorts_by_quarter=False, + has_sequence_qc=True, + ) + + def init_config(self): + self.config = { + "PUBLIC_RELEASES": ["1.0"], + "GENESET_GFF3_PATH": "reference/genome/AdirusWRAIR2/VectorBase-68_AdirusWRAIR2.gff.gz", + "GENOME_FASTA_PATH": "reference/genome/AdirusWRAIR2/VectorBase-56_AdirusWRAIR2_Genome.fasta", + "GENOME_FAI_PATH": "reference/genome/AdirusWRAIR2/VectorBase-56_AdirusWRAIR2_Genome.fasta.fai", + "GENOME_ZARR_PATH": "reference/genome/AdirusWRAIR2/VectorBase-56_AdirusWRAIR2_Genome.zarr", + "GENOME_REF_ID": "AdirusWRAIR2", + "GENOME_REF_NAME": "Anopheles dirus", + "CONTIGS": [ + "KB672490", + "KB672868", + "KB672979", + ], # Just using the three largest. + "SITE_ANNOTATIONS_ZARR_PATH": "reference/genome/AdirusWRAIR2/VectorBase-56_AdirusWRAIR2_Genome.SEQANNOTATION.zarr", + "DEFAULT_SITE_FILTERS_ANALYSIS": "sc_20250610", + "DEFAULT_COHORTS_ANALYSIS": "20250710", + "DEFAULT_DISCORDANT_READ_CALLS_ANALYSIS": "", + "SITE_MASK_IDS": ["dirus"], + "PHASING_ANALYSIS_IDS": ["dirus_noneyet"], + } + config_path = self.bucket_path / "v1.0-config.json" + with config_path.open(mode="w") as f: + json.dump(self.config, f, indent=4) + + def init_public_release_manifest(self): + # Here we create a release manifest for an Adir1-style + # public release. Note this is not the exact same data + # as the real release. + release_path = self.bucket_path / "v1.0" + release_path.mkdir(parents=True, exist_ok=True) + manifest_path = release_path / "manifest.tsv" + manifest = pd.DataFrame( + { + "sample_set": [ + "1277-VO-KH-WITKOWSKI-VMF00151", + "1276-AD-BD-ALAM-VMF00156", + ], + "sample_count": [20, 10], + "study_id": [ + "1277-VO-KH-WITKOWSKI", + "1276-AD-BD-ALAM", + ], + "study_url": [ + "https://www.malariagen.net/network/where-we-work/1277-VO-KH-WITKOWSKI", + "https://www.malariagen.net/network/where-we-work/1276-AD-BD-ALAM", + ], + "terms_of_use_expiry_date": [ + "2027-06-01", + "2027-06-01", + ], + "terms_of_use_url": [ + "https://malariagen.github.io/vector-data/adir1/adir1.0.html#terms-of-use", + "https://malariagen.github.io/vector-data/adir1/adir1.0.html#terms-of-use", + ], + } + ) + manifest.to_csv(manifest_path, index=False, sep="\t") + self.release_manifests["1.0"] = manifest + + def init_genome_sequence(self): + # Here we simulate a reference genome in a simple way + # but with much smaller contigs. The data are stored + # using zarr as with the real data releases. + + # Use real base composition. + base_composition = { + b"a": 0.0, + b"c": 0.0, + b"g": 0.0, + b"t": 0.0, + b"n": 0.0, + b"A": 0.29432128333333335, + b"C": 0.20542065, + b"G": 0.20575796666666665, + b"T": 0.2944834333333333, + b"N": 1.6666666666666667e-05, + } + path = self.bucket_path / self.config["GENOME_ZARR_PATH"] + self.genome = simulate_genome( + path=path, + contigs=self.contigs, + low=80_000, + high=120_000, + base_composition=base_composition, + ) + self.contig_sizes = { + contig: self.genome[contig].shape[0] for contig in self.contigs + } + + def init_genome_features(self): + path = self.bucket_path / self.config["GENESET_GFF3_PATH"] + path.parent.mkdir(parents=True, exist_ok=True) + simulator = Gff3Simulator( + contig_sizes=self.contig_sizes, + # Af1 has a different gene type + gene_type="protein_coding_gene", + # Af1 has different attributes + attrs=("Note", "description"), + ) + self.genome_features = simulator.simulate_gff(path=path) + + def write_metadata(self, release, release_path, sample_set, sequence_qc=True): + # Here we take the approach of using some of the real metadata, + # but truncating it to the number of samples included in the + # simulated data resource. + + # Look up the number of samples in this sample set within the + # simulated data resource. + n_samples_sim = ( + self.release_manifests[release] + .set_index("sample_set") + .loc[sample_set]["sample_count"] + ) + + # Create general metadata by sampling from some real metadata files. + src_path = ( + self.fixture_dir + / "vo_adir_release_master_us_central1" + / release_path + / "metadata" + / "general" + / sample_set + / "samples.meta.csv" + ) + df_general = pd.read_csv(src_path) + df_general_ds = df_general.sample(n_samples_sim, replace=False) + samples_ds = df_general_ds["sample_id"].tolist() + dst_path = ( + self.bucket_path + / release_path + / "metadata" + / "general" + / sample_set + / "samples.meta.csv" + ) + dst_path.parent.mkdir(parents=True, exist_ok=True) + df_general_ds.to_csv(dst_path, index=False) + + if sequence_qc: + # Create sequence QC metadata by sample from real metadata files. + src_path = ( + self.fixture_dir + / "vo_adir_release_master_us_central1" + / release_path + / "metadata" + / "curation" + / sample_set + / "sequence_qc_stats.csv" + ) + df_sequence_qc_stats = pd.read_csv(src_path) + df_sequence_qc_stats_ds = ( + df_sequence_qc_stats.set_index("sample_id") + .loc[samples_ds] + .reset_index() + ) + dst_path = ( + self.bucket_path + / release_path + / "metadata" + / "curation" + / sample_set + / "sequence_qc_stats.csv" + ) + dst_path.parent.mkdir(parents=True, exist_ok=True) + df_sequence_qc_stats_ds.to_csv(dst_path, index=False) + + # Create cohorts metadata by sampling from some real metadata files. + src_path = ( + self.fixture_dir + / "vo_adir_release_master_us_central1" + / release_path + / "metadata" + / "cohorts_20250710" + / sample_set + / "samples.cohorts.csv" + ) + df_coh = pd.read_csv(src_path) + df_coh_ds = df_coh.set_index("sample_id").loc[samples_ds].reset_index() + dst_path = ( + self.bucket_path + / release_path + / "metadata" + / "cohorts_20250710" + / sample_set + / "samples.cohorts.csv" + ) + dst_path.parent.mkdir(parents=True, exist_ok=True) + df_coh_ds.to_csv(dst_path, index=False) + + # Create data catalog by sampling from some real metadata files. + src_path = ( + self.fixture_dir + / "vo_adir_release_master_us_central1" + / release_path + / "metadata" + / "general" + / sample_set + / "wgs_snp_data.csv" + ) + df_cat = pd.read_csv(src_path) + df_cat_ds = df_cat.set_index("sample_id").loc[samples_ds].reset_index() + dst_path = ( + self.bucket_path + / release_path + / "metadata" + / "general" + / sample_set + / "wgs_snp_data.csv" + ) + dst_path.parent.mkdir(parents=True, exist_ok=True) + df_cat_ds.to_csv(dst_path, index=False) + + # # Create accessions catalog by sampling from some real metadata files. + # src_path = ( + # self.fixture_dir + # / "vo_adir_release_master_us_central1" + # / release_path + # / "metadata" + # / "general" + # / sample_set + # / "wgs_accession_data.csv" + # ) + # df_cat = pd.read_csv(src_path) + # df_cat_ds = df_cat.set_index("sample_id").loc[samples_ds].reset_index() + # dst_path = ( + # self.bucket_path + # / release_path + # / "metadata" + # / "general" + # / sample_set + # / "wgs_accession_data.csv" + # ) + # dst_path.parent.mkdir(parents=True, exist_ok=True) + # df_cat_ds.to_csv(dst_path, index=False) + + def init_metadata(self): + self.write_metadata( + release="1.0", + release_path="v1.0", + sample_set="1277-VO-KH-WITKOWSKI-VMF00151", + ) + self.write_metadata( + release="1.0", + release_path="v1.0", + sample_set="1276-AD-BD-ALAM-VMF00156", + ) + + def init_snp_sites(self): + path = self.bucket_path / "v1.0/snp_genotypes/all/sites/" + self.snp_sites, self.n_snp_sites = simulate_snp_sites( + path=path, contigs=self.contigs, genome=self.genome + ) + + def init_site_filters(self): + analysis = self.config["DEFAULT_SITE_FILTERS_ANALYSIS"] + + # Simulate the funestus mask. + mask = "dirus" + p_pass = 0.59 + path = self.bucket_path / "v1.0/site_filters" / analysis / mask + simulate_site_filters( + path=path, contigs=self.contigs, p_pass=p_pass, n_sites=self.n_snp_sites + ) + + def init_snp_genotypes(self): + # Iterate over releases. + for release, manifest in self.release_manifests.items(): + # Determine release path. + release_path = f"v{release}" + + # Iterate over sample sets in the release. + for rec in manifest.itertuples(): + sample_set = rec.sample_set + metadata_path = ( + self.bucket_path + / release_path + / "metadata" + / "general" + / sample_set + / "samples.meta.csv" + ) + + # Create zarr hierarchy. + zarr_path = ( + self.bucket_path + / release_path + / "snp_genotypes" + / "all" + / sample_set + ) + + # Simulate SNP genotype data. + p_allele = np.array([0.981, 0.006, 0.008, 0.005]) + p_missing = np.array([0.95, 0.05]) + simulate_snp_genotypes( + zarr_path=zarr_path, + metadata_path=metadata_path, + contigs=self.contigs, + n_sites=self.n_snp_sites, + p_allele=p_allele, + p_missing=p_missing, + ) + + def init_site_annotations(self): + path = self.bucket_path / self.config["SITE_ANNOTATIONS_ZARR_PATH"] + simulate_site_annotations(path=path, genome=self.genome) + + # For the following data fixtures we will use the "session" scope # so that the fixture data will be created only once per test # session (i.e., per invocation of pytest). @@ -2384,3 +2704,8 @@ def ag3_sim_fixture(fixture_dir): @pytest.fixture(scope="session") def af1_sim_fixture(fixture_dir): return Af1Simulator(fixture_dir=fixture_dir) + + +@pytest.fixture(scope="session") +def adir1_sim_fixture(fixture_dir): + return Adir1Simulator(fixture_dir=fixture_dir) diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.admin_units.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.admin_units.csv new file mode 100644 index 000000000..cfb109ef1 --- /dev/null +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.admin_units.csv @@ -0,0 +1,48 @@ +sample_id,country,country_ISO,adm1_name,adm1_ISO,adm2_name +VBS46299-6321STDY9453299,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46307-6321STDY9453307,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46315-6321STDY9453315,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46323-6321STDY9453323,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46331-6321STDY9453331,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46339-6321STDY9453339,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46300-6321STDY9453300,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46308-6321STDY9453308,Bangladesh,BGD,Chittagong 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Division,BD-B,Rangamati diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.cohorts.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.cohorts.csv new file mode 100644 index 000000000..23f0d4382 --- /dev/null +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.cohorts.csv @@ -0,0 +1,48 @@ +sample_id,country_ISO,adm1_name,adm1_ISO,adm2_name,taxon,cohort_admin1_year,cohort_admin1_month,cohort_admin1_quarter,cohort_admin2_year,cohort_admin2_month,cohort_admin2_quarter +VBS46299-6321STDY9453299,BGD,Chittagong Division,BD-B,Bandarban,baimaii,BD-B_baim_2018,BD-B_baim_2018_05,BD-B_baim_2018_Q2,BD-B_Bandarban_baim_2018,BD-B_Bandarban_baim_2018_05,BD-B_Bandarban_baim_2018_Q2 +VBS46307-6321STDY9453307,BGD,Chittagong 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b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.taxa.csv new file mode 100644 index 000000000..39284922d --- /dev/null +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.taxa.csv @@ -0,0 +1,27 @@ +sample_id,taxon +VBS45687-6143STDY8787412,dirus +VBS45688-6143STDY8787413,dirus +VBS45689-6143STDY8787414,dirus +VBS45690-6143STDY8787415,dirus +VBS45691-6143STDY8787416,dirus +VBS45692-6143STDY8787417,dirus +VBS45701-6143STDY8787420,dirus +VBS45702-6143STDY8787421,dirus +VBS45708-6143STDY8787424,dirus +VBS45709-6143STDY8787425,dirus +VBS45711-6143STDY8787426,dirus +VBS45713-6143STDY8787427,dirus +VBS45717-6143STDY8787429,dirus +VBS45718-6143STDY8787430,dirus +VBS45720-6143STDY8787431,dirus +VBS45723-6143STDY8787432,dirus +VBS45724-6143STDY8787433,dirus +VBS45728-6143STDY8787434,dirus +VBS45734-6143STDY8787435,dirus 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+@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesSampleMetadata( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + taxon_colors=_adir1.TAXON_COLORS, + ) + + +@pytest.fixture +def amin1_sim_api(amin1_sim_fixture): + return AnophelesSampleMetadata( + url=amin1_sim_fixture.url, + public_url=amin1_sim_fixture.url, + config_path=_amin1.CONFIG_PATH, + major_version_number=_amin1.MAJOR_VERSION_NUMBER, + major_version_path=_amin1.MAJOR_VERSION_PATH, + pre=False, + taxon_colors=_amin1.TAXON_COLORS, + ) + + @pytest.fixture def missing_metadata_api(fixture_dir): # In this fixture, one of the sample sets (AG1000G-BF-A) has missing files @@ -80,6 +108,14 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir_sim_api): + return adir1_sim_fixture, adir_sim_api + + +def case_amin1_sim(amin1_sim_fixture, amin1_sim_api): + return amin1_sim_fixture, amin1_sim_api + + def general_metadata_expected_columns(): return { "sample_id": "O", diff --git a/tests/anoph/test_snp_data.py b/tests/anoph/test_snp_data.py index ba4f1b690..453a6ccef 100644 --- a/tests/anoph/test_snp_data.py +++ b/tests/anoph/test_snp_data.py @@ -13,6 +13,8 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 + from malariagen_data.anoph.base_params import DEFAULT from malariagen_data.anoph.snp_data import AnophelesSnpData @@ -60,6 +62,23 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesSnpData( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + default_site_mask="dirus", + results_cache=adir1_sim_fixture.results_cache_path.as_posix(), + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for @@ -80,6 +99,10 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api + + @parametrize_with_cases("fixture,api", cases=".") def test_open_snp_sites(fixture, api: AnophelesSnpData): root = api.open_snp_sites() From 108743124f9a0f1ebba93d7e0eb781d5cc55e9db Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 4 Nov 2025 11:25:29 +1000 Subject: [PATCH 34/41] add coverage tests for adir1 --- tests/anoph/conftest.py | 44 ++-- .../samples.admin_units.csv | 48 ++++ .../samples.cohorts.csv | 48 ++++ .../1276-AD-BD-ALAM-VMF00156/samples.taxa.csv | 48 ++++ .../samples.admin_units.csv | 27 ++ .../samples.cohorts.csv | 27 ++ .../samples.taxa.csv | 27 ++ .../samples.admin_units.csv | 249 ++++++++++++++++++ .../samples.cohorts.csv | 249 ++++++++++++++++++ .../samples.taxa.csv | 249 ++++++++++++++++++ .../samples.admin_units.csv | 220 ++++++++++++++++ .../samples.cohorts.csv | 220 ++++++++++++++++ .../samples.taxa.csv | 220 ++++++++++++++++ .../sequence_qc_stats.csv | 48 ++++ .../sequence_qc_stats.csv | 27 ++ .../sequence_qc_stats.csv | 249 ++++++++++++++++++ .../sequence_qc_stats.csv | 220 ++++++++++++++++ .../1276-AD-BD-ALAM-VMF00156/samples.meta.csv | 48 ++++ .../sequence_qc_stats.csv | 48 ++++ .../wgs_accession_data.csv | 48 ++++ .../1276-AD-BD-ALAM-VMF00156/wgs_snp_data.csv | 48 ++++ .../samples.meta.csv | 27 ++ .../sequence_qc_stats.csv | 27 ++ .../wgs_accession_data.csv | 27 ++ .../wgs_snp_data.csv | 27 ++ .../samples.meta.csv | 249 ++++++++++++++++++ .../sequence_qc_stats.csv | 249 ++++++++++++++++++ .../wgs_accession_data.csv | 249 ++++++++++++++++++ .../wgs_snp_data.csv | 249 ++++++++++++++++++ .../samples.meta.csv | 220 ++++++++++++++++ .../sequence_qc_stats.csv | 220 ++++++++++++++++ .../wgs_accession_data.csv | 220 ++++++++++++++++ .../wgs_snp_data.csv | 220 ++++++++++++++++ .../samples.admin_units.csv | 249 ++++++++++++++++++ .../samples.cohorts.csv | 249 ++++++++++++++++++ .../samples.taxa.csv | 249 ++++++++++++++++++ .../samples.admin_units.csv | 220 ++++++++++++++++ .../samples.cohorts.csv | 220 ++++++++++++++++ .../samples.taxa.csv | 220 ++++++++++++++++ .../sequence_qc_stats.csv | 249 ++++++++++++++++++ .../sequence_qc_stats.csv | 220 ++++++++++++++++ .../1276-AD-BD-ALAM-VMF00156/samples.meta.csv | 96 +++---- .../sequence_qc_stats.csv | 96 +++---- .../wgs_accession_data.csv | 48 ++++ .../samples.meta.csv | 54 ++-- .../sequence_qc_stats.csv | 54 ++-- .../wgs_accession_data.csv | 27 ++ tests/anoph/test_base.py | 17 ++ tests/anoph/test_dipclust.py | 23 ++ tests/anoph/test_distance.py | 23 ++ tests/anoph/test_fst.py | 23 ++ tests/anoph/test_g123.py | 24 ++ tests/anoph/test_genome_features.py | 29 ++ tests/anoph/test_pca.py | 23 ++ tests/anoph/test_plink_converter.py | 20 ++ tests/anoph/test_sample_metadata.py | 22 +- tests/anoph/test_snp_frq.py | 24 ++ 57 files changed, 6683 insertions(+), 192 deletions(-) create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.admin_units.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.cohorts.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.taxa.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.admin_units.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.cohorts.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.taxa.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00183/samples.admin_units.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00183/samples.cohorts.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00183/samples.taxa.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1278-VO-TH-KOBYLINSKI-VMF00153/samples.admin_units.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1278-VO-TH-KOBYLINSKI-VMF00153/samples.cohorts.csv create mode 100644 tests/anoph/fixture/metadata/cohorts_20250710/1278-VO-TH-KOBYLINSKI-VMF00153/samples.taxa.csv create mode 100644 tests/anoph/fixture/metadata/curation/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/metadata/curation/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/samples.meta.csv create mode 100644 tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv create mode 100644 tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_snp_data.csv create mode 100644 tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/samples.meta.csv create mode 100644 tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv create mode 100644 tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_snp_data.csv create mode 100644 tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/samples.meta.csv create mode 100644 tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/wgs_accession_data.csv create mode 100644 tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/wgs_snp_data.csv create mode 100644 tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/samples.meta.csv create mode 100644 tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_accession_data.csv create mode 100644 tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_snp_data.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00183/samples.admin_units.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00183/samples.cohorts.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00183/samples.taxa.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1278-VO-TH-KOBYLINSKI-VMF00153/samples.admin_units.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1278-VO-TH-KOBYLINSKI-VMF00153/samples.cohorts.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/cohorts_20250710/1278-VO-TH-KOBYLINSKI-VMF00153/samples.taxa.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv diff --git a/tests/anoph/conftest.py b/tests/anoph/conftest.py index 7e7cd94d5..743191806 100644 --- a/tests/anoph/conftest.py +++ b/tests/anoph/conftest.py @@ -2588,28 +2588,28 @@ def write_metadata(self, release, release_path, sample_set, sequence_qc=True): dst_path.parent.mkdir(parents=True, exist_ok=True) df_cat_ds.to_csv(dst_path, index=False) - # # Create accessions catalog by sampling from some real metadata files. - # src_path = ( - # self.fixture_dir - # / "vo_adir_release_master_us_central1" - # / release_path - # / "metadata" - # / "general" - # / sample_set - # / "wgs_accession_data.csv" - # ) - # df_cat = pd.read_csv(src_path) - # df_cat_ds = df_cat.set_index("sample_id").loc[samples_ds].reset_index() - # dst_path = ( - # self.bucket_path - # / release_path - # / "metadata" - # / "general" - # / sample_set - # / "wgs_accession_data.csv" - # ) - # dst_path.parent.mkdir(parents=True, exist_ok=True) - # df_cat_ds.to_csv(dst_path, index=False) + # Create accessions catalog by sampling from some real metadata files. + src_path = ( + self.fixture_dir + / "vo_adir_release_master_us_central1" + / release_path + / "metadata" + / "general" + / sample_set + / "wgs_accession_data.csv" + ) + df_cat = pd.read_csv(src_path) + df_cat_ds = df_cat.set_index("sample_id").loc[samples_ds].reset_index() + dst_path = ( + self.bucket_path + / release_path + / "metadata" + / "general" + / sample_set + / "wgs_accession_data.csv" + ) + dst_path.parent.mkdir(parents=True, exist_ok=True) + df_cat_ds.to_csv(dst_path, index=False) def init_metadata(self): self.write_metadata( diff --git a/tests/anoph/fixture/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.admin_units.csv b/tests/anoph/fixture/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.admin_units.csv new file mode 100644 index 000000000..cfb109ef1 --- /dev/null +++ b/tests/anoph/fixture/metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.admin_units.csv @@ -0,0 +1,48 @@ +sample_id,country,country_ISO,adm1_name,adm1_ISO,adm2_name +VBS46299-6321STDY9453299,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46307-6321STDY9453307,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46315-6321STDY9453315,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46323-6321STDY9453323,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46331-6321STDY9453331,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46339-6321STDY9453339,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46300-6321STDY9453300,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46308-6321STDY9453308,Bangladesh,BGD,Chittagong Division,BD-B,Bandarban +VBS46316-6321STDY9453316,Bangladesh,BGD,Chittagong 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diff --git a/tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv b/tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv new file mode 100644 index 000000000..d7514da1a --- /dev/null +++ b/tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv @@ -0,0 +1,48 @@ +sample_id,run_ena +VBS46299-6321STDY9453299,"ERR5967855, ERR5967879, ERR5967903" +VBS46300-6321STDY9453300,"ERR5967861, ERR5967885, ERR5967909" +VBS46301-6321STDY9453301,"ERR5967867, ERR5967891, ERR5967915" +VBS46302-6321STDY9453302,"ERR5967873, ERR5967897, ERR5967921" +VBS46303-6321STDY9453303,"ERR6045486, ERR6045509, ERR6045532" +VBS46304-6321STDY9453304,"ERR6045492, ERR6045515, ERR6045538" +VBS46305-6321STDY9453305,"ERR6045498, ERR6045521, ERR6045544" +VBS46306-6321STDY9453306,"ERR6045504, ERR6045527, ERR6045550" +VBS46307-6321STDY9453307,"ERR5967856, ERR5967880, ERR5967904" +VBS46308-6321STDY9453308,"ERR5967862, ERR5967886, ERR5967910" +VBS46309-6321STDY9453309,"ERR5967868, ERR5967892, ERR5967916" +VBS46310-6321STDY9453310,"ERR5967874, ERR5967898, ERR5967922" +VBS46311-6321STDY9453311,"ERR6045487, ERR6045510, ERR6045533" +VBS46312-6321STDY9453312,"ERR6045493, ERR6045516, ERR6045539" +VBS46313-6321STDY9453313,"ERR6045499, ERR6045522, ERR6045545" +VBS46314-6321STDY9453314,"ERR6045505, ERR6045528, ERR6045551" +VBS46315-6321STDY9453315,"ERR5967857, ERR5967881, ERR5967905" +VBS46316-6321STDY9453316,"ERR5967863, ERR5967887, ERR5967911" +VBS46317-6321STDY9453317,"ERR5967869, ERR5967893, ERR5967917" +VBS46318-6321STDY9453318,"ERR5967875, ERR5967899, ERR5967923" +VBS46319-6321STDY9453319,"ERR6045488, ERR6045511, ERR6045534" +VBS46320-6321STDY9453320,"ERR6045494, ERR6045517, ERR6045540" +VBS46321-6321STDY9453321,"ERR6045500, ERR6045523, ERR6045546" +VBS46322-6321STDY9453322,"ERR6045506, ERR6045529, ERR6045552" +VBS46323-6321STDY9453323,"ERR5967858, ERR5967882, ERR5967906" +VBS46324-6321STDY9453324,"ERR5967864, ERR5967888, ERR5967912" +VBS46325-6321STDY9453325,"ERR5967870, ERR5967894, ERR5967918" +VBS46326-6321STDY9453326,"ERR5967876, ERR5967900, ERR5967924" +VBS46327-6321STDY9453327,"ERR6045489, ERR6045512, ERR6045535" +VBS46328-6321STDY9453328,"ERR6045495, ERR6045518, ERR6045541" +VBS46329-6321STDY9453329,"ERR6045501, ERR6045524, ERR6045547" +VBS46330-6321STDY9453330,"ERR6045507, ERR6045530, ERR6045553" +VBS46331-6321STDY9453331,"ERR5967859, ERR5967883, ERR5967907" +VBS46332-6321STDY9453332,"ERR5967865, ERR5967889, ERR5967913" +VBS46333-6321STDY9453333,"ERR5967871, ERR5967895, ERR5967919" +VBS46334-6321STDY9453334,"ERR5967877, ERR5967901, ERR5967925" +VBS46335-6321STDY9453335,"ERR6045490, ERR6045513, ERR6045536" +VBS46336-6321STDY9453336,"ERR6045496, ERR6045519, ERR6045542" +VBS46337-6321STDY9453337,"ERR6045502, ERR6045525, ERR6045548" +VBS46338-6321STDY9453338,"ERR6045508, ERR6045531, ERR6045554" +VBS46339-6321STDY9453339,"ERR5967860, ERR5967884, ERR5967908" +VBS46340-6321STDY9453340,"ERR5967866, ERR5967890, ERR5967914" +VBS46341-6321STDY9453341,"ERR5967872, ERR5967896, ERR5967920" +VBS46342-6321STDY9453342,"ERR5967878, ERR5967902, ERR5967926" +VBS46343-6321STDY9453343,"ERR6045491, ERR6045514, ERR6045537" +VBS46344-6321STDY9453344,"ERR6045497, ERR6045520, ERR6045543" +VBS46345-6321STDY9453345,"ERR6045503, ERR6045526, ERR6045549" diff --git a/tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_snp_data.csv b/tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_snp_data.csv new file mode 100644 index 000000000..77f8712ef --- /dev/null +++ b/tests/anoph/fixture/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_snp_data.csv @@ -0,0 +1,48 @@ +sample_id,alignments_bam,alignments_bam_md5,snp_genotypes_vcf,snp_genotypes_vcf_md5,snp_genotypes_zarr,snp_genotypes_zarr_md5,pipeline_version +VBS46299-6321STDY9453299,https://1276-ad-bd-alam-vmf00156.cog.sanger.ac.uk/VBS46299-6321STDY9453299.bam,b99888ef49680a23d2c2eb99d9a76d8b,https://1276-ad-bd-alam-vmf00156.cog.sanger.ac.uk/VBS46299-6321STDY9453299.vcf.gz,881fbba998d25a3e66aead2439ce2e02,https://1276-ad-bd-alam-vmf00156.cog.sanger.ac.uk/VBS46299-6321STDY9453299.zarr.zip,3dedee4185f663fe81803e86eef4596d,https://github.com/malariagen/pipelines/tree/ec02c42b5632da96ad549fd23dd49e7fdfeebd17 +VBS46307-6321STDY9453307,https://1276-ad-bd-alam-vmf00156.cog.sanger.ac.uk/VBS46307-6321STDY9453307.bam,918618042d01773378fc346f655d8cf4,https://1276-ad-bd-alam-vmf00156.cog.sanger.ac.uk/VBS46307-6321STDY9453307.vcf.gz,ffc30b183b452593d5f4e7470a7812f2,https://1276-ad-bd-alam-vmf00156.cog.sanger.ac.uk/VBS46307-6321STDY9453307.zarr.zip,df7daea5845e6400208ab0b7baed24be,https://github.com/malariagen/pipelines/tree/ec02c42b5632da96ad549fd23dd49e7fdfeebd17 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a/tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv b/tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv new file mode 100644 index 000000000..6618ab19d --- /dev/null +++ b/tests/anoph/fixture/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv @@ -0,0 +1,249 @@ +,sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence +0,VBS54551-6143STDY11462443,24.37,24,24,24.35,24,24,24.47,24,24,24.41,24,24,24.11,24,23,24.46,24,24,0.982,0.01406 +1,VBS54553-6143STDY11462445,25.31,25,25,25.39,25,25,25.53,25,25,25.8,26,25,24.26,24,23,25.34,25,24,0.983,0.01392 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a/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/samples.meta.csv b/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/samples.meta.csv new file mode 100644 index 000000000..542879be1 --- /dev/null +++ b/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/samples.meta.csv @@ -0,0 +1,220 @@ +sample_id,derived_sample_id,partner_sample_id,contributor,country,location,year,month,latitude,longitude,taxon,sex_call +VBS45974-6296STDY9478582,VBS45974-6296STDY9478582,329,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, A",2019,2,9.110,98.878,dirus,UKN +VBS45976-6296STDY9478584,VBS45976-6296STDY9478584,339,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, A/2",2019,2,9.110,98.878,dirus,UKN +VBS45979-6296STDY9478587,VBS45979-6296STDY9478587,920,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, C2",2019,3,9.134,98.888,dirus,UKN +VBS45982-6296STDY9478589,VBS45982-6296STDY9478589,1007,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, C2",2019,4,9.134,98.888,dirus,UKN +VBS46005-6296STDY9478612,VBS46005-6296STDY9478612,1845,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46042-6296STDY9478649,VBS46042-6296STDY9478649,2014,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS46050-6296STDY9478657,VBS46050-6296STDY9478657,2043,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46059-6296STDY9478666,VBS46059-6296STDY9478666,2523,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,dirus,UKN +VBS46066-6296STDY9478673,VBS46066-6296STDY9478673,2909,Kevin Kobylinski,Thailand,"Phanom, three, C1",2019,6,8.890,98.664,dirus,UKN +VBS46067-6296STDY9478674,VBS46067-6296STDY9478674,2935,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,dirus,UKN +VBS46078-6296STDY9478687,VBS46078-6296STDY9478687,3109,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,dirus,UKN +VBS46083-6296STDY9478692,VBS46083-6296STDY9478692,3185,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,dirus,UKN +VBS46084-6296STDY9478693,VBS46084-6296STDY9478693,3191,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,dirus,UKN +VBS46087-6296STDY9478696,VBS46087-6296STDY9478696,3325,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,dirus,UKN +VBS46088-6296STDY9478697,VBS46088-6296STDY9478697,3330,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,dirus,UKN +VBS46098-6296STDY9478707,VBS46098-6296STDY9478707,3932_1278,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,3,9.340,98.880,dirus,UKN +VBS46121-6296STDY9478730,VBS46121-6296STDY9478730,4591,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,dirus,UKN +VBS46141-6296STDY9478750,VBS46141-6296STDY9478750,5202,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46145-6296STDY9478754,VBS46145-6296STDY9478754,5206,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46146-6296STDY9478755,VBS46146-6296STDY9478755,5209,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46154-6296STDY9478763,VBS46154-6296STDY9478763,5221,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46168-6296STDY9478779,VBS46168-6296STDY9478779,5244,Kevin Kobylinski,Thailand,"Vibhavadi, six, A",2019,10,9.252,98.850,dirus,UKN +VBS46172-6296STDY9478782,VBS46172-6296STDY9478782,5265,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,10,9.340,98.880,dirus,UKN +VBS46173-6296STDY9478783,VBS46173-6296STDY9478783,5313,Kevin Kobylinski,Thailand,"Vibhavadi, ten, F",2019,10,9.353,98.875,dirus,UKN +VBS46175-6296STDY9478785,VBS46175-6296STDY9478785,5496,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,dirus,UKN +VBS46180-6296STDY9478790,VBS46180-6296STDY9478790,5506_1278,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,dirus,UKN +VBS46183-6296STDY9478793,VBS46183-6296STDY9478793,5592,Kevin Kobylinski,Thailand,"Vibhavadi, eight, I",2019,10,9.296,98.886,dirus,UKN +VBS46187-6296STDY9478797,VBS46187-6296STDY9478797,5614,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,dirus,UKN +VBS46188-6296STDY9478798,VBS46188-6296STDY9478798,5619,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,dirus,UKN +VBS46189-6296STDY9478799,VBS46189-6296STDY9478799,5647,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,dirus,UKN +VBS46190-6296STDY9478800,VBS46190-6296STDY9478800,5649,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,dirus,UKN +VBS46192-6296STDY9478801,VBS46192-6296STDY9478801,5683,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, N",2019,10,9.083,98.878,dirus,UKN +VBS46198-6296STDY9478807,VBS46198-6296STDY9478807,5736,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,dirus,UKN +VBS45975-6296STDY10244530,VBS45975-6296STDY10244530,331,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, A",2019,2,9.110,98.878,dirus,UKN +VBS45983-6296STDY10244537,VBS45983-6296STDY10244537,1200,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, C1",2019,4,9.080,98.879,dirus,UKN +VBS45984-6296STDY10244538,VBS45984-6296STDY10244538,1363,Kevin Kobylinski,Thailand,"Phanom, three, A2",2019,4,8.894,98.667,dirus,UKN +VBS45985-6296STDY10244539,VBS45985-6296STDY10244539,1364,Kevin Kobylinski,Thailand,"Phanom, three, A2",2019,4,8.894,98.667,dirus,UKN +VBS45986-6296STDY10244540,VBS45986-6296STDY10244540,1494,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, D1",2019,4,9.107,98.869,dirus,UKN +VBS45987-6296STDY10244541,VBS45987-6296STDY10244541,1498,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, D2",2019,4,9.107,98.869,dirus,UKN +VBS45988-6296STDY10244542,VBS45988-6296STDY10244542,1687,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS45989-6296STDY10244543,VBS45989-6296STDY10244543,1688,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS45991-6296STDY10244545,VBS45991-6296STDY10244545,1711,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS45992-6296STDY10244546,VBS45992-6296STDY10244546,1719,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS45993-6296STDY10244547,VBS45993-6296STDY10244547,1738,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS45994-6296STDY10244548,VBS45994-6296STDY10244548,1750,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS45995-6296STDY10244549,VBS45995-6296STDY10244549,1759,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS45996-6296STDY10244550,VBS45996-6296STDY10244550,1771,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS45997-6296STDY10244551,VBS45997-6296STDY10244551,1774,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS45998-6296STDY10244552,VBS45998-6296STDY10244552,1780,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS45999-6296STDY10244553,VBS45999-6296STDY10244553,1793,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS46000-6296STDY10244554,VBS46000-6296STDY10244554,1810,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46001-6296STDY10244555,VBS46001-6296STDY10244555,1818,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46002-6296STDY10244556,VBS46002-6296STDY10244556,1826_1278,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46003-6296STDY10244557,VBS46003-6296STDY10244557,1830,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46004-6296STDY10244558,VBS46004-6296STDY10244558,1840,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46006-6296STDY10244560,VBS46006-6296STDY10244560,1854,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46007-6296STDY10244561,VBS46007-6296STDY10244561,1859,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46008-6296STDY10244562,VBS46008-6296STDY10244562,1860,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46009-6296STDY10244563,VBS46009-6296STDY10244563,1866,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46010-6296STDY10244564,VBS46010-6296STDY10244564,1871,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46011-6296STDY10244565,VBS46011-6296STDY10244565,1872,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46012-6296STDY10244566,VBS46012-6296STDY10244566,1875,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46013-6296STDY10244567,VBS46013-6296STDY10244567,1881,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46014-6296STDY10244568,VBS46014-6296STDY10244568,1887,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46016-6296STDY10244570,VBS46016-6296STDY10244570,1908,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46017-6296STDY10244571,VBS46017-6296STDY10244571,1912,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46019-6296STDY10244573,VBS46019-6296STDY10244573,1931,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46020-6296STDY10244574,VBS46020-6296STDY10244574,1932,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46021-6296STDY10244575,VBS46021-6296STDY10244575,1934,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46022-6296STDY10244576,VBS46022-6296STDY10244576,1936,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46025-6296STDY10244579,VBS46025-6296STDY10244579,1946,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46026-6296STDY10244580,VBS46026-6296STDY10244580,1949,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46027-6296STDY10244581,VBS46027-6296STDY10244581,1950,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46028-6296STDY10244582,VBS46028-6296STDY10244582,1951,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46029-6296STDY10244583,VBS46029-6296STDY10244583,1954,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46030-6296STDY10244584,VBS46030-6296STDY10244584,1956,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46031-6296STDY10244585,VBS46031-6296STDY10244585,1960,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46032-6296STDY10244586,VBS46032-6296STDY10244586,1966,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46033-6296STDY10244587,VBS46033-6296STDY10244587,1975,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46034-6296STDY10244588,VBS46034-6296STDY10244588,1977,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46035-6296STDY10244589,VBS46035-6296STDY10244589,1978,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46036-6296STDY10244590,VBS46036-6296STDY10244590,1989,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,dirus,UKN +VBS46037-6296STDY10244591,VBS46037-6296STDY10244591,1999,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS46038-6296STDY10244592,VBS46038-6296STDY10244592,2000,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS46039-6296STDY10244593,VBS46039-6296STDY10244593,2003,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS46040-6296STDY10244594,VBS46040-6296STDY10244594,2006,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS46041-6296STDY10244595,VBS46041-6296STDY10244595,2011,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS46043-6296STDY10244597,VBS46043-6296STDY10244597,2017,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS46044-6296STDY10244598,VBS46044-6296STDY10244598,2018,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,dirus,UKN +VBS46045-6296STDY10244599,VBS46045-6296STDY10244599,2028,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46046-6296STDY10244600,VBS46046-6296STDY10244600,2037,Kevin Kobylinski,Thailand,"Phanom, three, B2",2019,5,8.896,98.663,dirus,UKN +VBS46047-6296STDY10244601,VBS46047-6296STDY10244601,2039,Kevin Kobylinski,Thailand,"Phanom, three, B2",2019,5,8.896,98.663,dirus,UKN +VBS46048-6296STDY10244602,VBS46048-6296STDY10244602,2040,Kevin Kobylinski,Thailand,"Phanom, three, B2",2019,5,8.896,98.663,dirus,UKN +VBS46049-6296STDY10244603,VBS46049-6296STDY10244603,2041,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46051-6296STDY10244605,VBS46051-6296STDY10244605,2044,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46052-6296STDY10244606,VBS46052-6296STDY10244606,2045,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46053-6296STDY10244607,VBS46053-6296STDY10244607,2047,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,dirus,UKN +VBS46054-6296STDY10244608,VBS46054-6296STDY10244608,2431,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E1",2019,5,9.068,98.846,dirus,UKN +VBS46055-6296STDY10244609,VBS46055-6296STDY10244609,2444,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,dirus,UKN +VBS46056-6296STDY10244610,VBS46056-6296STDY10244610,2499,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,dirus,UKN +VBS46057-6296STDY10244611,VBS46057-6296STDY10244611,2503,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,dirus,UKN +VBS46060-6296STDY10244614,VBS46060-6296STDY10244614,2569,Kevin Kobylinski,Thailand,"Vibhavadi, eleven, A",2019,5,9.360,98.876,dirus,UKN +VBS46061-6296STDY10244615,VBS46061-6296STDY10244615,2688,Kevin Kobylinski,Thailand,"Vibhavadi, nine, A3",2019,1,9.331,98.878,dirus,UKN +VBS46063-6296STDY10244617,VBS46063-6296STDY10244617,2841,Kevin Kobylinski,Thailand,"Phanom, three, C2",2019,6,8.890,98.663,dirus,UKN +VBS46064-6296STDY10244618,VBS46064-6296STDY10244618,2889,Kevin Kobylinski,Thailand,"Phanom, three, C1",2019,6,8.890,98.664,dirus,UKN +VBS46065-6296STDY10244619,VBS46065-6296STDY10244619,2894,Kevin Kobylinski,Thailand,"Phanom, three, C1",2019,6,8.890,98.664,dirus,UKN +VBS46068-6296STDY10244622,VBS46068-6296STDY10244622,2937,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,dirus,UKN +VBS46069-6296STDY10244625,VBS46069-6296STDY10244625,2944,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,dirus,UKN +VBS46070-6296STDY10244626,VBS46070-6296STDY10244626,2960,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,dirus,UKN +VBS46071-6296STDY10244627,VBS46071-6296STDY10244627,2961,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,dirus,UKN +VBS46072-6296STDY10244628,VBS46072-6296STDY10244628,3007,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,dirus,UKN +VBS46073-6296STDY10244629,VBS46073-6296STDY10244629,3037,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, H",2019,6,9.136,98.881,dirus,UKN +VBS46074-6296STDY10244630,VBS46074-6296STDY10244630,3041,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, H",2019,6,9.136,98.881,dirus,UKN +VBS46075-6296STDY10244631,VBS46075-6296STDY10244631,3062,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,dirus,UKN +VBS46076-6296STDY10244632,VBS46076-6296STDY10244632,3077,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,dirus,UKN +VBS46077-6296STDY10244633,VBS46077-6296STDY10244633,3079,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,dirus,UKN +VBS46079-6296STDY10244635,VBS46079-6296STDY10244635,3129,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, G",2019,6,9.135,98.882,dirus,UKN +VBS46080-6296STDY10244636,VBS46080-6296STDY10244636,3142,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, G",2019,6,9.063,98.877,dirus,UKN +VBS46081-6296STDY10244637,VBS46081-6296STDY10244637,3170,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,dirus,UKN +VBS46082-6296STDY10244638,VBS46082-6296STDY10244638,3183,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,dirus,UKN +VBS46085-6296STDY10244641,VBS46085-6296STDY10244641,3249,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,dirus,UKN +VBS46086-6296STDY10244642,VBS46086-6296STDY10244642,3316,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,dirus,UKN +VBS46089-6296STDY10244645,VBS46089-6296STDY10244645,3388,Kevin Kobylinski,Thailand,"Vibhavadi, eight, B1",2019,7,9.304,98.885,dirus,UKN +VBS46090-6296STDY10244646,VBS46090-6296STDY10244646,3396,Kevin Kobylinski,Thailand,"Vibhavadi, eight, B1",2019,7,9.304,98.885,dirus,UKN +VBS46091-6296STDY10244647,VBS46091-6296STDY10244647,3397,Kevin Kobylinski,Thailand,"Vibhavadi, eight, B2",2019,7,9.304,98.886,dirus,UKN +VBS46092-6296STDY10244648,VBS46092-6296STDY10244648,3581,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, H",2019,7,9.110,98.880,dirus,UKN +VBS46093-6296STDY10244649,VBS46093-6296STDY10244649,3623,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, I",2019,7,9.052,98.865,dirus,UKN +VBS46094-6296STDY10244650,VBS46094-6296STDY10244650,3710,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, I",2019,7,9.140,98.881,dirus,UKN +VBS46095-6296STDY10244651,VBS46095-6296STDY10244651,3745,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, I",2019,7,9.052,98.865,dirus,UKN +VBS46096-6296STDY10244652,VBS46096-6296STDY10244652,3780,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,7,9.082,98.861,dirus,UKN +VBS46097-6296STDY10244653,VBS46097-6296STDY10244653,3840,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,3,9.340,98.880,dirus,UKN +VBS46099-6296STDY10244655,VBS46099-6296STDY10244655,3954,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,3,9.340,98.880,dirus,UKN +VBS46100-6296STDY10244656,VBS46100-6296STDY10244656,4148,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, J",2019,8,9.111,98.881,dirus,UKN +VBS46101-6296STDY10244657,VBS46101-6296STDY10244657,4149,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, J",2019,8,9.111,98.881,dirus,UKN +VBS46102-6296STDY10244658,VBS46102-6296STDY10244658,4151,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, J",2019,8,9.111,98.881,dirus,UKN +VBS46103-6296STDY10244659,VBS46103-6296STDY10244659,4156_1278,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, I",2019,8,9.105,98.889,dirus,UKN +VBS46104-6296STDY10244660,VBS46104-6296STDY10244660,4235,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, M",2019,8,9.126,98.903,dirus,UKN +VBS46105-6296STDY10244661,VBS46105-6296STDY10244661,4274,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, I",2019,8,9.105,98.889,dirus,UKN +VBS46106-6296STDY10244662,VBS46106-6296STDY10244662,4310,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,dirus,UKN +VBS46107-6296STDY10244663,VBS46107-6296STDY10244663,4321,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,dirus,UKN +VBS46108-6296STDY10244664,VBS46108-6296STDY10244664,4407,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, K",2019,8,9.084,98.876,dirus,UKN +VBS46109-6296STDY10244665,VBS46109-6296STDY10244665,4430,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, K",2019,8,9.084,98.876,dirus,UKN +VBS46110-6296STDY10244666,VBS46110-6296STDY10244666,4472,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, J",2019,8,9.053,98.852,dirus,UKN +VBS46111-6296STDY10244667,VBS46111-6296STDY10244667,4488,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, K",2019,8,9.052,98.857,dirus,UKN +VBS46112-6296STDY10244668,VBS46112-6296STDY10244668,4511,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, K",2019,8,9.084,98.876,dirus,UKN +VBS46113-6296STDY10244669,VBS46113-6296STDY10244669,4556,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,dirus,UKN +VBS46114-6296STDY10244670,VBS46114-6296STDY10244670,4560,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,dirus,UKN +VBS46115-6296STDY10244671,VBS46115-6296STDY10244671,4577,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,dirus,UKN +VBS46116-6296STDY10244672,VBS46116-6296STDY10244672,4578,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,dirus,UKN +VBS46117-6296STDY10244673,VBS46117-6296STDY10244673,4579,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,dirus,UKN +VBS46118-6296STDY10244674,VBS46118-6296STDY10244674,4585,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,dirus,UKN +VBS46119-6296STDY10244675,VBS46119-6296STDY10244675,4589,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,dirus,UKN +VBS46120-6296STDY10244676,VBS46120-6296STDY10244676,4590,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,dirus,UKN +VBS46122-6296STDY10244678,VBS46122-6296STDY10244678,4596,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,dirus,UKN +VBS46123-6296STDY10244679,VBS46123-6296STDY10244679,4609,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,dirus,UKN +VBS46124-6296STDY10244680,VBS46124-6296STDY10244680,4666,Kevin Kobylinski,Thailand,"Vibhavadi, eight, F",2019,2,9.307,98.885,dirus,UKN +VBS46125-6296STDY10244681,VBS46125-6296STDY10244681,4768,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,dirus,UKN +VBS46126-6296STDY10244682,VBS46126-6296STDY10244682,4778,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,dirus,UKN +VBS46127-6296STDY10244683,VBS46127-6296STDY10244683,4779,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,dirus,UKN +VBS46128-6296STDY10244684,VBS46128-6296STDY10244684,4788,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,dirus,UKN +VBS46129-6296STDY10244685,VBS46129-6296STDY10244685,4809,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,dirus,UKN +VBS46130-6296STDY10244686,VBS46130-6296STDY10244686,4875,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,2,9.340,98.880,dirus,UKN +VBS46131-6296STDY10244687,VBS46131-6296STDY10244687,5191_1278,Kevin Kobylinski,Thailand,"Phanom, one, F",2019,10,8.869,98.638,dirus,UKN +VBS46132-6296STDY10244688,VBS46132-6296STDY10244688,5192,Kevin Kobylinski,Thailand,"Phanom, one, F",2019,10,8.869,98.638,dirus,UKN +VBS46133-6296STDY10244689,VBS46133-6296STDY10244689,5194,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46134-6296STDY10244690,VBS46134-6296STDY10244690,5195,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46135-6296STDY10244691,VBS46135-6296STDY10244691,5196,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46136-6296STDY10244692,VBS46136-6296STDY10244692,5197,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46137-6296STDY10244693,VBS46137-6296STDY10244693,5198,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46138-6296STDY10244694,VBS46138-6296STDY10244694,5199,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46139-6296STDY10244695,VBS46139-6296STDY10244695,5200,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46140-6296STDY10244696,VBS46140-6296STDY10244696,5201,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46142-6296STDY10244698,VBS46142-6296STDY10244698,5203,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46143-6296STDY10244699,VBS46143-6296STDY10244699,5204,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46144-6296STDY10244700,VBS46144-6296STDY10244700,5205,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46147-6296STDY10244703,VBS46147-6296STDY10244703,5214,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46148-6296STDY10244704,VBS46148-6296STDY10244704,5215,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46149-6296STDY10244705,VBS46149-6296STDY10244705,5216,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46150-6296STDY10244706,VBS46150-6296STDY10244706,5217,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46151-6296STDY10244707,VBS46151-6296STDY10244707,5218,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46152-6296STDY10244708,VBS46152-6296STDY10244708,5219,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46153-6296STDY10244709,VBS46153-6296STDY10244709,5220,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46155-6296STDY10244711,VBS46155-6296STDY10244711,5222,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46156-6296STDY10244712,VBS46156-6296STDY10244712,5223,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46157-6296STDY10244713,VBS46157-6296STDY10244713,5226,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46158-6296STDY10244714,VBS46158-6296STDY10244714,5227,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46160-6296STDY10244716,VBS46160-6296STDY10244716,5230_1278,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46161-6296STDY10244717,VBS46161-6296STDY10244717,5231,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,dirus,UKN +VBS46162-6296STDY10244718,VBS46162-6296STDY10244718,5232,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46163-6296STDY10244721,VBS46163-6296STDY10244721,5233,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46164-6296STDY10244722,VBS46164-6296STDY10244722,5236,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46165-6296STDY10244723,VBS46165-6296STDY10244723,5237,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46166-6296STDY10244724,VBS46166-6296STDY10244724,5238,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,dirus,UKN +VBS46170-6296STDY10244727,VBS46170-6296STDY10244727,5247,Kevin Kobylinski,Thailand,"Vibhavadi, nine, D",2019,10,9.327,98.877,dirus,UKN +VBS46171-6296STDY10244728,VBS46171-6296STDY10244728,5248,Kevin Kobylinski,Thailand,"Vibhavadi, nine, D",2019,10,9.327,98.877,dirus,UKN +VBS46174-6296STDY10244731,VBS46174-6296STDY10244731,5494,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,dirus,UKN +VBS46176-6296STDY10244733,VBS46176-6296STDY10244733,5500,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,dirus,UKN +VBS46177-6296STDY10244734,VBS46177-6296STDY10244734,5501,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,dirus,UKN +VBS46178-6296STDY10244735,VBS46178-6296STDY10244735,5502,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,dirus,UKN +VBS46179-6296STDY10244736,VBS46179-6296STDY10244736,5505,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,dirus,UKN +VBS46181-6296STDY10244738,VBS46181-6296STDY10244738,5542,Kevin Kobylinski,Thailand,"Vibhavadi, eight, I",2019,10,9.296,98.886,dirus,UKN +VBS46182-6296STDY10244739,VBS46182-6296STDY10244739,5548,Kevin Kobylinski,Thailand,"Vibhavadi, eight, I",2019,10,9.296,98.886,dirus,UKN +VBS46184-6296STDY10244741,VBS46184-6296STDY10244741,5604,Kevin Kobylinski,Thailand,"Khirirat Nikhom, five, B",2019,10,9.043,98.894,dirus,UKN +VBS46185-6296STDY10244742,VBS46185-6296STDY10244742,5609,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,dirus,UKN +VBS46186-6296STDY10244743,VBS46186-6296STDY10244743,5613,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,dirus,UKN +VBS46193-6296STDY10244749,VBS46193-6296STDY10244749,5697,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, O",2019,10,9.076,98.868,dirus,UKN +VBS46194-6296STDY10244750,VBS46194-6296STDY10244750,5721,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,dirus,UKN +VBS46195-6296STDY10244751,VBS46195-6296STDY10244751,5725,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,dirus,UKN +VBS46196-6296STDY10244752,VBS46196-6296STDY10244752,5727,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,dirus,UKN +VBS46197-6296STDY10244753,VBS46197-6296STDY10244753,5728,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,dirus,UKN +VBS46199-6296STDY10244755,VBS46199-6296STDY10244755,5738,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,dirus,UKN +VBS46200-6296STDY10244756,VBS46200-6296STDY10244756,5765,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, K",2019,10,9.108,98.875,dirus,UKN +VBS46201-6296STDY10244757,VBS46201-6296STDY10244757,5771,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, K",2019,10,9.108,98.875,dirus,UKN +VBS46202-6296STDY10244758,VBS46202-6296STDY10244758,5777,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, L",2019,10,9.109,98.877,dirus,UKN +VBS46203-6296STDY10244759,VBS46203-6296STDY10244759,5895,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, Q",2019,10,9.127,98.905,dirus,UKN +VBS46204-6296STDY10244760,VBS46204-6296STDY10244760,5972,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, M",2019,10,9.104,98.891,dirus,UKN +VBS46205-6296STDY10244761,VBS46205-6296STDY10244761,6024,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, M",2019,10,9.104,98.891,dirus,UKN +VBS46206-6296STDY10244762,VBS46206-6296STDY10244762,6036,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, N",2019,10,9.106,98.887,dirus,UKN +VBS46207-6296STDY10244763,VBS46207-6296STDY10244763,6037,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, N",2019,10,9.106,98.887,dirus,UKN diff --git a/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv b/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv new file mode 100644 index 000000000..d6c6cebde --- /dev/null +++ b/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv @@ -0,0 +1,220 @@ +,sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence +0,VBS45974-6296STDY9478582,9.79,9,9,9.79,9,9,9.81,9,9,9.91,10,9,9.81,9,9,9.62,9,9,0.952,0.03652 +1,VBS45975-6296STDY10244530,75.33,76,75,74.27,74,75,74.89,75,75,76.6,76,75,76.95,78,77,74.97,75,75,0.959,0.03382 +2,VBS45976-6296STDY9478584,12.9,13,12,12.95,13,12,12.87,13,12,13.16,13,12,12.6,12,12,12.83,13,12,0.952,0.03517 +3,VBS45979-6296STDY9478587,14.53,14,14,14.56,14,14,14.39,14,14,14.72,14,14,14.56,14,14,14.42,14,14,0.954,0.03525 +5,VBS45982-6296STDY9478589,20.34,19,18,20.91,20,19,20.46,19,18,20.86,20,18,19.02,18,17,19.81,19,18,0.955,0.03414 +6,VBS45983-6296STDY10244537,16.39,16,16,16.38,16,16,16.34,16,16,16.93,17,16,16.07,16,16,16.19,16,16,0.955,0.03482 +7,VBS45984-6296STDY10244538,36.46,37,37,36.39,36,36,36.38,36,37,37.05,37,37,36.14,36,37,36.36,36,37,0.957,0.03366 +8,VBS45985-6296STDY10244539,37.61,38,38,37.81,38,38,37.37,37,38,38.91,39,38,36.55,37,36,37.22,37,37,0.957,0.03361 +9,VBS45986-6296STDY10244540,42.12,42,42,42.54,43,42,42.04,42,42,43.8,44,43,40.26,41,41,41.4,42,41,0.956,0.03393 +10,VBS45987-6296STDY10244541,37.26,37,37,37.56,37,37,37.37,37,37,38.76,39,38,35.6,36,36,36.47,37,36,0.957,0.03383 +11,VBS45988-6296STDY10244542,38.39,39,39,38.55,39,39,38.36,38,39,39.36,39,39,37.31,38,38,38.11,38,39,0.958,0.03386 +12,VBS45989-6296STDY10244543,49.81,50,50,49.82,50,50,49.57,50,50,51.36,51,51,48.79,49,49,49.44,50,50,0.957,0.03365 +13,VBS45991-6296STDY10244545,45.77,46,46,46.01,46,47,45.76,46,46,47.23,47,47,44.29,45,46,45.2,46,46,0.958,0.03387 +14,VBS45992-6296STDY10244546,37.63,38,38,37.58,38,37,37.6,38,38,38.71,39,38,36.73,37,37,37.43,37,37,0.957,0.03359 +15,VBS45993-6296STDY10244547,38.07,38,38,38.01,38,38,37.95,38,38,39.0,39,39,37.58,38,38,37.81,38,38,0.957,0.03362 +16,VBS45994-6296STDY10244548,44.41,45,45,44.32,44,44,44.24,44,44,45.33,45,45,43.8,44,45,44.44,45,45,0.957,0.03363 +17,VBS45995-6296STDY10244549,38.14,38,38,37.9,38,38,38.13,38,39,39.34,39,39,37.46,38,38,37.94,38,38,0.955,0.03396 +18,VBS45996-6296STDY10244550,36.73,37,37,36.41,36,36,36.66,37,36,37.77,38,37,36.51,37,37,36.47,37,37,0.957,0.0336 +19,VBS45997-6296STDY10244551,76.86,78,79,77.22,78,79,76.63,78,79,79.64,80,81,74.05,76,77,76.28,77,78,0.959,0.03383 +20,VBS45998-6296STDY10244552,64.83,65,66,65.01,65,65,65.03,65,65,66.89,67,67,62.63,64,65,64.1,65,65,0.959,0.03395 +21,VBS45999-6296STDY10244553,45.76,46,46,45.75,46,46,45.62,46,46,48.71,49,49,43.74,44,45,44.72,45,45,0.958,0.03387 +22,VBS46000-6296STDY10244554,89.13,90,91,89.65,91,92,88.16,90,90,93.33,94,93,85.9,88,90,88.3,90,89,0.959,0.03382 +23,VBS46001-6296STDY10244555,35.07,35,35,34.88,35,35,35.04,35,35,36.13,36,36,34.34,34,35,35.01,35,35,0.957,0.03358 +24,VBS46002-6296STDY10244556,40.42,40,39,40.36,40,38,40.37,40,39,41.57,41,40,39.71,39,38,40.07,39,39,0.957,0.03366 +25,VBS46003-6296STDY10244557,42.55,42,41,42.5,42,41,42.5,42,41,44.01,44,42,41.62,41,40,41.99,42,41,0.957,0.03363 +26,VBS46004-6296STDY10244558,42.06,42,42,42.35,42,42,42.17,42,42,44.16,44,44,39.92,40,41,41.1,41,41,0.958,0.03388 +27,VBS46005-6296STDY9478612,18.82,18,18,18.97,19,18,18.76,18,18,19.12,19,18,18.45,18,17,18.67,18,18,0.955,0.0338 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+166,VBS46148-6296STDY10244704,31.45,31,31,31.35,31,31,31.57,31,31,32.63,32,32,30.76,31,31,30.8,31,31,0.957,0.03377 +167,VBS46149-6296STDY10244705,29.1,29,28,29.34,29,28,29.23,29,28,30.06,29,28,27.87,27,27,28.6,28,27,0.957,0.03379 +168,VBS46150-6296STDY10244706,20.8,20,20,20.7,20,20,20.86,20,20,21.32,21,20,20.65,20,20,20.44,20,20,0.956,0.03391 +169,VBS46151-6296STDY10244707,24.77,24,24,24.71,24,24,24.61,24,24,25.36,25,24,24.69,24,24,24.6,24,24,0.955,0.0336 +170,VBS46152-6296STDY10244708,32.49,32,32,32.36,32,32,32.22,32,32,33.6,33,33,32.24,32,32,32.15,32,32,0.956,0.03356 +171,VBS46153-6296STDY10244709,29.23,29,29,28.99,29,29,29.2,29,29,29.9,30,29,29.23,29,29,28.96,29,29,0.956,0.03359 +172,VBS46154-6296STDY9478763,22.68,22,21,22.87,22,22,22.64,22,21,23.02,23,22,22.21,22,21,22.45,22,21,0.956,0.03394 +173,VBS46155-6296STDY10244711,24.16,24,23,24.19,24,23,24.08,24,23,24.95,25,24,23.88,23,23,23.63,23,23,0.956,0.03396 +174,VBS46156-6296STDY10244712,118.65,121,121,118.98,121,121,118.33,120,121,121.77,122,122,115.98,120,122,117.72,120,120,0.961,0.03411 +175,VBS46157-6296STDY10244713,25.58,25,25,25.45,25,25,25.64,25,25,26.32,26,25,25.37,25,25,25.11,25,24,0.957,0.03381 +176,VBS46158-6296STDY10244714,36.8,37,38,36.79,37,38,36.25,37,38,38.96,39,39,35.64,37,38,36.49,37,39,0.95,0.03358 +178,VBS46160-6296STDY10244716,28.45,28,28,28.36,28,28,28.24,28,28,29.21,29,28,28.3,28,28,28.27,28,28,0.956,0.0336 +179,VBS46161-6296STDY10244717,38.22,38,38,38.25,38,38,38.05,38,38,39.23,39,39,37.73,38,38,37.79,38,38,0.957,0.03361 +180,VBS46162-6296STDY10244718,24.72,25,24,24.86,25,24,24.67,24,24,25.57,25,25,24.07,24,24,24.21,24,24,0.957,0.03379 +181,VBS46163-6296STDY10244721,29.39,29,29,29.51,29,29,29.38,29,29,30.52,30,30,28.5,29,29,28.8,29,29,0.957,0.03376 +182,VBS46164-6296STDY10244722,35.79,36,36,35.61,36,36,35.65,36,36,37.05,37,37,35.46,35,35,35.26,35,35,0.957,0.03358 +183,VBS46165-6296STDY10244723,39.2,39,39,39.39,39,39,38.79,39,39,40.44,40,40,38.57,39,39,38.76,39,38,0.957,0.03367 +184,VBS46166-6296STDY10244724,26.63,26,26,26.52,26,26,26.52,26,26,26.97,27,26,26.58,26,27,26.7,26,26,0.955,0.03352 +185,VBS46168-6296STDY9478779,17.34,17,16,17.35,17,16,17.46,17,16,17.75,17,16,16.99,16,15,17.04,16,16,0.954,0.03396 +186,VBS46170-6296STDY10244727,36.15,36,35,36.26,36,35,36.07,36,35,37.16,37,36,35.31,35,34,35.76,35,35,0.956,0.03363 +187,VBS46171-6296STDY10244728,31.95,32,32,31.97,32,32,32.18,32,32,32.76,32,32,31.3,31,31,31.29,31,31,0.957,0.03378 +188,VBS46172-6296STDY9478782,25.51,24,23,25.62,24,23,25.5,24,22,25.76,24,23,25.37,24,23,25.14,24,23,0.955,0.03366 +189,VBS46173-6296STDY9478783,28.84,26,21,30.4,27,22,29.01,26,21,29.66,26,22,25.82,22,19,27.77,25,21,0.956,0.034 +190,VBS46174-6296STDY10244731,32.13,32,32,31.84,32,32,31.88,32,32,33.84,34,33,31.58,31,31,31.76,32,31,0.957,0.03362 +191,VBS46175-6296STDY9478785,18.43,18,17,18.7,18,17,18.52,18,17,18.76,18,17,17.76,17,16,18.11,18,17,0.956,0.03414 +192,VBS46176-6296STDY10244733,24.01,23,23,23.95,23,23,24.07,23,23,24.5,24,24,23.75,23,23,23.78,23,23,0.957,0.0337 +193,VBS46177-6296STDY10244734,30.57,30,30,30.28,30,30,30.35,30,30,32.09,32,32,30.11,30,30,30.25,30,30,0.956,0.03355 +194,VBS46178-6296STDY10244735,29.16,29,29,29.07,29,28,29.16,29,29,30.54,30,30,28.5,28,29,28.42,28,28,0.957,0.03378 +195,VBS46179-6296STDY10244736,41.43,41,41,41.79,42,42,41.52,41,41,42.91,43,42,39.89,40,40,40.47,41,40,0.958,0.03383 +196,VBS46180-6296STDY9478790,27.45,27,26,28.0,27,26,27.43,27,26,27.99,27,26,26.13,25,24,27.21,27,26,0.955,0.03357 +197,VBS46181-6296STDY10244738,37.58,37,37,37.67,37,37,37.3,37,37,38.8,39,38,36.84,37,37,37.24,37,37,0.956,0.0336 +198,VBS46182-6296STDY10244739,34.23,33,30,34.34,33,30,34.19,33,30,34.02,33,30,34.2,32,30,34.39,33,30,0.958,0.03393 +199,VBS46183-6296STDY9478793,28.95,28,27,29.58,29,27,29.16,28,27,29.98,29,27,27.12,26,25,28.06,27,26,0.954,0.03397 +200,VBS46184-6296STDY10244741,40.2,40,40,40.35,40,40,39.87,40,40,41.49,41,41,39.27,39,40,39.92,40,40,0.957,0.03364 +201,VBS46185-6296STDY10244742,37.54,38,38,37.23,37,37,37.36,37,37,38.8,39,39,37.14,37,38,37.39,37,38,0.957,0.03361 +202,VBS46186-6296STDY10244743,38.08,38,38,37.73,37,37,38.0,38,37,39.1,39,38,38.08,38,38,37.74,38,38,0.957,0.03366 +203,VBS46187-6296STDY9478797,31.02,30,30,31.43,31,30,30.97,30,30,31.47,31,30,30.07,30,30,30.75,30,30,0.958,0.0338 +204,VBS46188-6296STDY9478798,33.01,33,32,33.28,33,32,32.97,33,32,33.35,33,32,32.36,32,32,32.86,33,32,0.958,0.03381 +205,VBS46189-6296STDY9478799,17.99,17,14,18.68,17,15,17.97,17,15,18.17,17,14,16.8,15,13,17.67,16,14,0.954,0.03431 +206,VBS46190-6296STDY9478800,33.69,34,33,34.08,34,34,33.65,34,33,34.39,34,34,32.53,32,32,33.4,33,33,0.956,0.03355 +207,VBS46192-6296STDY9478801,20.39,19,18,20.83,20,19,20.36,19,18,20.77,20,18,19.54,18,17,20.03,19,18,0.954,0.03387 +208,VBS46193-6296STDY10244749,28.05,28,27,28.18,28,28,28.04,28,28,29.4,29,28,26.87,27,27,27.48,27,27,0.957,0.03377 +209,VBS46194-6296STDY10244750,31.1,31,30,31.16,31,30,30.96,31,30,31.8,31,30,30.61,30,30,30.91,31,30,0.956,0.03359 +210,VBS46195-6296STDY10244751,33.61,33,33,33.31,33,33,33.34,33,33,35.37,35,35,32.93,33,33,33.33,33,33,0.956,0.03356 +211,VBS46196-6296STDY10244752,47.5,48,47,47.63,48,48,47.36,47,47,49.55,49,49,46.18,47,47,46.53,47,47,0.959,0.03387 +212,VBS46197-6296STDY10244753,45.85,46,45,46.01,46,45,46.14,46,45,47.77,47,47,44.18,44,44,44.6,44,44,0.958,0.03387 +213,VBS46198-6296STDY9478807,34.31,34,33,34.5,34,33,34.5,34,33,34.88,34,34,33.46,33,33,33.87,34,33,0.958,0.03386 +214,VBS46199-6296STDY10244755,40.36,40,41,40.34,40,40,40.22,40,41,42.19,42,42,39.22,40,40,39.72,40,40,0.958,0.03382 +215,VBS46200-6296STDY10244756,39.17,39,39,38.79,39,39,39.02,39,39,40.98,41,41,38.61,39,39,38.69,39,38,0.957,0.03363 +216,VBS46201-6296STDY10244757,35.86,36,36,36.06,36,36,35.85,36,36,37.81,38,37,34.23,34,34,34.92,35,35,0.958,0.03384 +217,VBS46202-6296STDY10244758,31.32,31,31,31.34,31,31,30.88,31,31,32.76,33,32,30.78,31,31,30.89,31,31,0.955,0.03393 +218,VBS46203-6296STDY10244759,35.76,36,36,35.88,36,35,35.78,36,36,37.41,37,37,34.51,35,35,34.92,35,35,0.958,0.03386 +219,VBS46204-6296STDY10244760,38.65,39,38,38.57,38,38,38.6,38,38,39.15,39,39,38.39,38,39,38.6,38,38,0.957,0.03363 +220,VBS46205-6296STDY10244761,39.33,39,39,39.14,39,39,39.03,39,39,40.71,41,41,38.74,39,39,39.19,39,39,0.957,0.03365 +221,VBS46206-6296STDY10244762,40.58,41,41,40.65,41,40,40.55,41,40,42.95,43,43,38.93,39,40,39.49,40,40,0.958,0.03385 +222,VBS46207-6296STDY10244763,34.64,35,35,34.36,34,34,34.66,35,34,36.07,36,35,34.07,34,34,34.07,34,34,0.956,0.03361 diff --git a/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_accession_data.csv b/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_accession_data.csv new file mode 100644 index 000000000..d33bbbb77 --- /dev/null +++ b/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_accession_data.csv @@ -0,0 +1,220 @@ +sample_id,run_ena +VBS45974-6296STDY9478582,"ERR6280005, ERR6280039, ERR6280073" +VBS45975-6296STDY10244530,"ERR6280107, ERR6280138, ERR6280169" +VBS45976-6296STDY9478584,"ERR6280006, ERR6280040, ERR6280074" +VBS45979-6296STDY9478587,"ERR6197341, ERR6197375, ERR6197409" +VBS45982-6296STDY9478589,"ERR6197343, ERR6197377, ERR6197411" +VBS45983-6296STDY10244537,"ERR6280199, ERR6280230, ERR6280263" +VBS45984-6296STDY10244538,"ERR6280200, ERR6280231, ERR6280264" +VBS45985-6296STDY10244539,"ERR6280108, ERR6280139, ERR6280170" +VBS45986-6296STDY10244540,"ERR6280299, ERR6280329, ERR6280359" +VBS45987-6296STDY10244541,"ERR6280201, ERR6280232, ERR6280265" +VBS45988-6296STDY10244542,"ERR6280202, ERR6280233, ERR6280266" +VBS45989-6296STDY10244543,"ERR6280300, ERR6280330, ERR6280360" +VBS45991-6296STDY10244545,"ERR6280301, ERR6280331, ERR6280361" +VBS45992-6296STDY10244546,"ERR6280203, ERR6280235, ERR6280268" +VBS45993-6296STDY10244547,"ERR6280302, ERR6280332, ERR6280362" +VBS45994-6296STDY10244548,"ERR6280303, ERR6280333, ERR6280363" +VBS45995-6296STDY10244549,"ERR6280204, ERR6280236, ERR6280269" +VBS45996-6296STDY10244550,"ERR6280112, ERR6280143, ERR6280174" +VBS45997-6296STDY10244551,"ERR6280304, ERR6280334, ERR6280364" +VBS45998-6296STDY10244552,"ERR6280205, ERR6280237, ERR6280270" +VBS45999-6296STDY10244553,"ERR6280113, ERR6280144, ERR6280175" +VBS46000-6296STDY10244554,"ERR6280307, ERR6280337, ERR6280367" +VBS46001-6296STDY10244555,"ERR6280115, ERR6280146, ERR6280177" +VBS46002-6296STDY10244556,"ERR6280206, ERR6280238, ERR6280271" +VBS46003-6296STDY10244557,"ERR6280310, ERR6280340, ERR6280370" +VBS46004-6296STDY10244558,"ERR6280207, ERR6280239, ERR6280272" +VBS46005-6296STDY9478612,"ERR6280311, ERR6280341, ERR6280371" +VBS46006-6296STDY10244560,"ERR6280116, ERR6280147, ERR6280178" +VBS46007-6296STDY10244561,"ERR6280208, ERR6280240, ERR6280273" +VBS46008-6296STDY10244562,"ERR6280117, ERR6280148, ERR6280179" +VBS46009-6296STDY10244563,"ERR6280118, ERR6280149, ERR6280180" +VBS46010-6296STDY10244564,"ERR6280313, ERR6280343, ERR6280373" +VBS46011-6296STDY10244565,"ERR6280209, ERR6280241, ERR6280274" +VBS46012-6296STDY10244566,"ERR6280314, ERR6280344, ERR6280374" +VBS46013-6296STDY10244567,"ERR6280210, ERR6280242, ERR6280275" +VBS46014-6296STDY10244568,"ERR6280119, ERR6280150, ERR6280181" +VBS46016-6296STDY10244570,"ERR6280211, ERR6280243, ERR6280276" +VBS46017-6296STDY10244571,"ERR6280212, ERR6280244, ERR6280277" +VBS46019-6296STDY10244573,"ERR6280316, ERR6280346, ERR6280376" +VBS46020-6296STDY10244574,"ERR6280213, ERR6280245, ERR6280278" +VBS46021-6296STDY10244575,"ERR6280317, ERR6280347, ERR6280377" +VBS46022-6296STDY10244576,"ERR6280120, ERR6280151, ERR6280182" +VBS46025-6296STDY10244579,"ERR6280214, ERR6280247, ERR6280280" +VBS46026-6296STDY10244580,"ERR6280215, ERR6280248, ERR6280281" +VBS46027-6296STDY10244581,"ERR6280216, ERR6280249, ERR6280282" +VBS46028-6296STDY10244582,"ERR6280217, ERR6280250, ERR6280283" +VBS46029-6296STDY10244583,"ERR6280121, ERR6280152, ERR6280183" +VBS46030-6296STDY10244584,"ERR6280122, ERR6280153, ERR6280184" +VBS46031-6296STDY10244585,"ERR6280218, ERR6280251, ERR6280284" +VBS46032-6296STDY10244586,"ERR6280123, ERR6280154, ERR6280185" +VBS46033-6296STDY10244587,"ERR6280219, ERR6280252, ERR6280285" +VBS46034-6296STDY10244588,"ERR6280124, ERR6280155, ERR6280186" +VBS46035-6296STDY10244589,"ERR6280220, ERR6280253, ERR6280286" +VBS46036-6296STDY10244590,"ERR6280125, ERR6280156, ERR6280187" +VBS46037-6296STDY10244591,"ERR6280126, ERR6280157, ERR6280188" +VBS46038-6296STDY10244592,"ERR6280127, ERR6280158, ERR6280189" +VBS46039-6296STDY10244593,"ERR6280128, ERR6280159, ERR6280190" +VBS46040-6296STDY10244594,"ERR6280129, ERR6280160, ERR6280191" +VBS46041-6296STDY10244595,"ERR6280130, ERR6280161, ERR6280192" +VBS46042-6296STDY9478649,"ERR6280319, ERR6280349, ERR6280379" +VBS46043-6296STDY10244597,"ERR6280221, ERR6280254, ERR6280287" +VBS46044-6296STDY10244598,"ERR6280320, ERR6280350, ERR6280380" +VBS46045-6296STDY10244599,"ERR6280222, ERR6280255, ERR6280288" +VBS46046-6296STDY10244600,"ERR6280223, ERR6280256, ERR6280289" +VBS46047-6296STDY10244601,"ERR6280224, ERR6280257, ERR6280290" +VBS46048-6296STDY10244602,"ERR6280131, ERR6280162, ERR6280193" +VBS46049-6296STDY10244603,"ERR6280132, ERR6280163, ERR6280194" +VBS46050-6296STDY9478657,"ERR6280032, ERR6280066, ERR6280100" +VBS46051-6296STDY10244605,"ERR6280225, ERR6280258, ERR6280291" +VBS46052-6296STDY10244606,"ERR6280133, ERR6280164, ERR6280195" +VBS46053-6296STDY10244607,"ERR6280226, ERR6280259, ERR6280292" +VBS46054-6296STDY10244608,"ERR6280227, ERR6280260, ERR6280293" +VBS46055-6296STDY10244609,"ERR6280321, ERR6280351, ERR6280381" +VBS46056-6296STDY10244610,"ERR6280134, ERR6280165, ERR6280196" +VBS46057-6296STDY10244611,"ERR6280322, ERR6280352, ERR6280382" +VBS46059-6296STDY9478666,"ERR6280036, ERR6280070, ERR6280104" +VBS46060-6296STDY10244614,"ERR6280135, ERR6280166, ERR6280197" +VBS46061-6296STDY10244615,"ERR6280323, ERR6280353, ERR6280383" +VBS46063-6296STDY10244617,"ERR6280324, ERR6280354, ERR6280384" +VBS46064-6296STDY10244618,"ERR6280136, ERR6280167, ERR6336419" +VBS46065-6296STDY10244619,"ERR6280137, ERR6280168, ERR6280198" +VBS46066-6296STDY9478673,"ERR6280325, ERR6280355, ERR6280385" +VBS46067-6296STDY9478674,"ERR6280038, ERR6280072, ERR6280106" +VBS46068-6296STDY10244622,"ERR6280229, ERR6280262, ERR6280295" +VBS46069-6296STDY10244625,"ERR6197443, ERR6197478, ERR6279970" +VBS46070-6296STDY10244626,"ERR6197444, ERR6197479, ERR6279971" +VBS46071-6296STDY10244627,"ERR6197445, ERR6197480, ERR6279972" +VBS46072-6296STDY10244628,"ERR6197446, ERR6197481, ERR6279973" +VBS46073-6296STDY10244629,"ERR6280007, ERR6280041, ERR6280075" +VBS46074-6296STDY10244630,"ERR6280008, ERR6280042, ERR6280076" +VBS46075-6296STDY10244631,"ERR6197342, ERR6197376, ERR6197410" +VBS46076-6296STDY10244632,"ERR6280010, ERR6280044, ERR6280078" +VBS46077-6296STDY10244633,"ERR6280011, ERR6280045, ERR6280079" +VBS46078-6296STDY9478687,"ERR6280012, ERR6280046, ERR6280080" +VBS46079-6296STDY10244635,"ERR6197447, ERR6197482, ERR6279974" +VBS46080-6296STDY10244636,"ERR6197344, ERR6197378, ERR6197412" +VBS46081-6296STDY10244637,"ERR6197448, ERR6197483, ERR6279975" +VBS46082-6296STDY10244638,"ERR6197345, ERR6197379, ERR6197413" +VBS46083-6296STDY9478692,"ERR6280013, ERR6280047, ERR6280081" +VBS46084-6296STDY9478693,"ERR6280014, ERR6280048, ERR6280082" +VBS46085-6296STDY10244641,"ERR6197346, ERR6197380, ERR6197414" +VBS46086-6296STDY10244642,"ERR6197347, ERR6197381, ERR6197415" +VBS46087-6296STDY9478696,"ERR6280015, ERR6280049, ERR6280083" +VBS46088-6296STDY9478697,"ERR6280016, ERR6280050, ERR6280084" +VBS46089-6296STDY10244645,"ERR6197449, ERR6197484, ERR6279976" +VBS46090-6296STDY10244646,"ERR6197450, ERR6197485, ERR6279977" +VBS46091-6296STDY10244647,"ERR6197451, ERR6197486, ERR6279978" +VBS46092-6296STDY10244648,"ERR6197452, ERR6197487, ERR6279979" +VBS46093-6296STDY10244649,"ERR6197348, ERR6197382, ERR6197416" +VBS46094-6296STDY10244650,"ERR6197453, ERR6197488, ERR6279980" +VBS46095-6296STDY10244651,"ERR6197454, ERR6197489, ERR6279981" +VBS46096-6296STDY10244652,"ERR6197455, ERR6197490, ERR6279982" +VBS46097-6296STDY10244653,"ERR6280017, ERR6280051, ERR6280085" +VBS46098-6296STDY9478707,"ERR6280018, ERR6280052, ERR6280086" +VBS46099-6296STDY10244655,"ERR6197456, ERR6197491, ERR6279983" +VBS46100-6296STDY10244656,"ERR6197349, ERR6197383, ERR6197417" +VBS46101-6296STDY10244657,"ERR6197457, ERR6197492, ERR6279984" +VBS46102-6296STDY10244658,"ERR6280019, ERR6280053, ERR6280087" +VBS46103-6296STDY10244659,"ERR6197350, ERR6197384, ERR6197418" +VBS46104-6296STDY10244660,"ERR6197458, ERR6197493, ERR6279985" +VBS46105-6296STDY10244661,"ERR6197459, ERR6197494, ERR6279986" +VBS46106-6296STDY10244662,"ERR6197460, ERR6197495, ERR6279987" +VBS46107-6296STDY10244663,"ERR6197461, ERR6197496, ERR6279988" +VBS46108-6296STDY10244664,"ERR6280020, ERR6280054, ERR6280088" +VBS46109-6296STDY10244665,"ERR6280021, ERR6280055, ERR6280089" +VBS46110-6296STDY10244666,"ERR6280022, ERR6280056, ERR6280090" +VBS46111-6296STDY10244667,"ERR6197462, ERR6197497, ERR6279989" +VBS46112-6296STDY10244668,"ERR6280023, ERR6280057, ERR6280091" +VBS46113-6296STDY10244669,"ERR6280024, ERR6280058, ERR6280092" +VBS46114-6296STDY10244670,"ERR6197463, ERR6197498, ERR6279990" +VBS46115-6296STDY10244671,"ERR6280025, ERR6280059, ERR6280093" +VBS46116-6296STDY10244672,"ERR6280026, ERR6280060, ERR6280094" +VBS46117-6296STDY10244673,"ERR6280027, ERR6280061, ERR6280095" +VBS46118-6296STDY10244674,"ERR6280028, ERR6280062, ERR6280096" +VBS46119-6296STDY10244675,"ERR6197464, ERR6197499, ERR6279991" +VBS46120-6296STDY10244676,"ERR6197351, ERR6197385, ERR6197419" +VBS46121-6296STDY9478730,"ERR6280029, ERR6280063, ERR6280097" +VBS46122-6296STDY10244678,"ERR6197352, ERR6197386, ERR6197420" +VBS46123-6296STDY10244679,"ERR6197465, ERR6197500, ERR6279992" +VBS46124-6296STDY10244680,"ERR6197466, ERR6197501, ERR6279993" +VBS46125-6296STDY10244681,"ERR6197467, ERR6197502, ERR6279994" +VBS46126-6296STDY10244682,"ERR6197468, ERR6197503, ERR6279995" +VBS46127-6296STDY10244683,"ERR6280030, ERR6280064, ERR6280098" +VBS46128-6296STDY10244684,"ERR6197353, ERR6197387, ERR6197421" +VBS46129-6296STDY10244685,"ERR6197469, ERR6197504, ERR6279996" +VBS46130-6296STDY10244686,"ERR6197470, ERR6197505, ERR6279997" +VBS46131-6296STDY10244687,"ERR6197354, ERR6197388, ERR6197422" +VBS46132-6296STDY10244688,"ERR6197355, ERR6197389, ERR6197423" +VBS46133-6296STDY10244689,"ERR6197356, ERR6197390, ERR6197424" +VBS46134-6296STDY10244690,"ERR6197357, ERR6197391, ERR6197425" +VBS46135-6296STDY10244691,"ERR6197358, ERR6197392, ERR6197426" +VBS46136-6296STDY10244692,"ERR6197359, ERR6197393, ERR6197427" +VBS46137-6296STDY10244693,"ERR6197360, ERR6197394, ERR6197428" +VBS46138-6296STDY10244694,"ERR6197471, ERR6197506, ERR6279998" +VBS46139-6296STDY10244695,"ERR6197472, ERR6197507, ERR6279999" +VBS46140-6296STDY10244696,"ERR6197361, ERR6197395, ERR6197429" +VBS46141-6296STDY9478750,"ERR6280031, ERR6280065, ERR6280099" +VBS46142-6296STDY10244698,"ERR6197362, ERR6197396, ERR6197430" +VBS46143-6296STDY10244699,"ERR6197473, ERR6197508, ERR6280000" +VBS46144-6296STDY10244700,"ERR6197363, ERR6197397, ERR6197431" +VBS46145-6296STDY9478754,"ERR6280033, ERR6280067, ERR6280101" +VBS46146-6296STDY9478755,"ERR6280034, ERR6280068, ERR6280102" +VBS46147-6296STDY10244703,"ERR6197474, ERR6197509, ERR6280001" +VBS46148-6296STDY10244704,"ERR6197364, ERR6197398, ERR6197432" +VBS46149-6296STDY10244705,"ERR6197365, ERR6197399, ERR6197433" +VBS46150-6296STDY10244706,"ERR6197366, ERR6197400, ERR6197434" +VBS46151-6296STDY10244707,"ERR6197367, ERR6197401, ERR6197435" +VBS46152-6296STDY10244708,"ERR6197475, ERR6197510, ERR6280002" +VBS46153-6296STDY10244709,"ERR6197368, ERR6197402, ERR6197436" +VBS46154-6296STDY9478763,"ERR6280037, ERR6280071, ERR6280105" +VBS46155-6296STDY10244711,"ERR6197369, ERR6197403, ERR6197437" +VBS46156-6296STDY10244712,"ERR6197370, ERR6197404, ERR6197438" +VBS46157-6296STDY10244713,"ERR6197371, ERR6197405, ERR6197439" +VBS46158-6296STDY10244714,"ERR6197372, ERR6197406, ERR6197440" +VBS46160-6296STDY10244716,"ERR6197476, ERR6197511, ERR6280003" +VBS46161-6296STDY10244717,"ERR6197477, ERR6197512, ERR6280004" +VBS46162-6296STDY10244718,"ERR6197374, ERR6197408, ERR6197442" +VBS46163-6296STDY10244721,"ERR6197251, ERR6197281, ERR6197311" +VBS46164-6296STDY10244722,"ERR6197252, ERR6197282, ERR6197312" +VBS46165-6296STDY10244723,"ERR6197253, ERR6197283, ERR6197313" +VBS46166-6296STDY10244724,"ERR6197254, ERR6197284, ERR6197314" +VBS46168-6296STDY9478779,"ERR6280296, ERR6280326, ERR6280356" +VBS46170-6296STDY10244727,"ERR6197255, ERR6197285, ERR6197315" +VBS46171-6296STDY10244728,"ERR6197256, ERR6197286, ERR6197316" +VBS46172-6296STDY9478782,"ERR6280297, ERR6280327, ERR6280357" +VBS46173-6296STDY9478783,"ERR6280298, ERR6280328, ERR6280358" +VBS46174-6296STDY10244731,"ERR6197257, ERR6197287, ERR6197317" +VBS46175-6296STDY9478785,"ERR6280109, ERR6280140, ERR6280171" +VBS46176-6296STDY10244733,"ERR6197258, ERR6197288, ERR6197318" +VBS46177-6296STDY10244734,"ERR6197259, ERR6197289, ERR6197319" +VBS46178-6296STDY10244735,"ERR6197260, ERR6197290, ERR6197320" +VBS46179-6296STDY10244736,"ERR6197261, ERR6197291, ERR6197321" +VBS46180-6296STDY9478790,"ERR6280110, ERR6280141, ERR6280172" +VBS46181-6296STDY10244738,"ERR6197262, ERR6197292, ERR6197322" +VBS46182-6296STDY10244739,"ERR6197263, ERR6197293, ERR6197323" +VBS46183-6296STDY9478793,"ERR6280111, ERR6280142, ERR6280173" +VBS46184-6296STDY10244741,"ERR6197264, ERR6197294, ERR6197324" +VBS46185-6296STDY10244742,"ERR6197265, ERR6197295, ERR6197325" +VBS46186-6296STDY10244743,"ERR6197266, ERR6197296, ERR6197326" +VBS46187-6296STDY9478797,"ERR6280305, ERR6280335, ERR6280365" +VBS46188-6296STDY9478798,"ERR6280306, ERR6280336, ERR6280366" +VBS46189-6296STDY9478799,"ERR6280114, ERR6280145, ERR6280176" +VBS46190-6296STDY9478800,"ERR6280308, ERR6280338, ERR6280368" +VBS46192-6296STDY9478801,"ERR6280309, ERR6280339, ERR6280369" +VBS46193-6296STDY10244749,"ERR6197267, ERR6197297, ERR6197327" +VBS46194-6296STDY10244750,"ERR6197268, ERR6197298, ERR6197328" +VBS46195-6296STDY10244751,"ERR6197269, ERR6197299, ERR6197329" +VBS46196-6296STDY10244752,"ERR6197270, ERR6197300, ERR6197330" +VBS46197-6296STDY10244753,"ERR6197271, ERR6197301, ERR6197331" +VBS46198-6296STDY9478807,"ERR6280312, ERR6280342, ERR6280372" +VBS46199-6296STDY10244755,"ERR6197272, ERR6197302, ERR6197332" +VBS46200-6296STDY10244756,"ERR6197273, ERR6197303, ERR6197333" +VBS46201-6296STDY10244757,"ERR6197274, ERR6197304, ERR6197334" +VBS46202-6296STDY10244758,"ERR6197275, ERR6197305, ERR6197335" +VBS46203-6296STDY10244759,"ERR6197276, ERR6197306, ERR6197336" +VBS46204-6296STDY10244760,"ERR6197277, ERR6197307, ERR6197337" +VBS46205-6296STDY10244761,"ERR6197278, ERR6197308, ERR6197338" +VBS46206-6296STDY10244762,"ERR6197279, ERR6197309, ERR6197339" +VBS46207-6296STDY10244763,"ERR6197280, ERR6197310, ERR6197340" diff --git a/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_snp_data.csv b/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_snp_data.csv new file mode 100644 index 000000000..8f116bb46 --- /dev/null +++ b/tests/anoph/fixture/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_snp_data.csv @@ -0,0 +1,220 @@ +sample_id,alignments_bam,alignments_bam_md5,snp_genotypes_vcf,snp_genotypes_vcf_md5,snp_genotypes_zarr,snp_genotypes_zarr_md5,pipeline_version +VBS45974-6296STDY9478582,https://1278-vo-th-kobylinski-vmf00153.cog.sanger.ac.uk/VBS45974-6296STDY9478582.bam,1adeaa92579eed7a46af285f3ba77859,https://1278-vo-th-kobylinski-vmf00153.cog.sanger.ac.uk/VBS45974-6296STDY9478582.vcf.gz,f3a02b70a2043b08169a20c0411d6018,https://1278-vo-th-kobylinski-vmf00153.cog.sanger.ac.uk/VBS45974-6296STDY9478582.zarr.zip,d20d2ee334391c43ff9e9004da373d4a,https://github.com/malariagen/pipelines/tree/ec02c42b5632da96ad549fd23dd49e7fdfeebd17 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a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv new file mode 100644 index 000000000..6618ab19d --- /dev/null +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv @@ -0,0 +1,249 @@ +,sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence +0,VBS54551-6143STDY11462443,24.37,24,24,24.35,24,24,24.47,24,24,24.41,24,24,24.11,24,23,24.46,24,24,0.982,0.01406 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+VBS46345-6321STDY9453345,67.62,68,69,69.4,70,71,75.11,75,75,71.31,39,250,37.02,31,30,60.14,63,63,79.29,78,74,81.78,55,250,65.89,68,5,74.79,61,2,53.74,47,2,99.31,104,250,85.17,85,82,64.04,65,66,40.71,41,2,53.28,41,5,56.48,48,3,68.76,72,75,51.1,33,250,85.14,57,250,48.82,50,3,134.13,142,250,126.68,88,250,65.45,67,69,111.4,80,250,58.1,56,2,134.55,126,250,75.56,47,250,61.15,63,67,72.55,61,250,81.61,44,250,157.89,198,250,223.95,250,250,107.91,67,250,63.79,66,67,74.13,73,69,62.86,61,68,58.69,53,250,67.04,53,2,78.62,54,250,52.02,51,57,68.01,59,250,40.35,39,42,49.17,50,71,53.77,59,61,65.34,67,68,49,50,72,46.7,46,33,52.11,41,7,51.85,37,2,56.5,61,60,55.03,32,2,62.65,50,250,113.6,105,250,66.46,53,2,53.61,56,59,68.97,70,71,54.14,58,63,43.21,41,27,83.66,42,250,62.93,68,73,76.73,65,5,59.09,38,250,54.5,57,62,138.05,157,250,70.83,24,250,71.3,72,74,78.57,41,250,17.54,10,3,118.9,68,250,69.76,55,250,74.97,52,25,127.62,144,250,63.9,41,2,103.27,59,250,64.39,66,67,64.52,59,61,101.35,58,250,46.61,47,50,66.65,35,250,128.03,103,250,65.48,67,68,95.17,57,250,144.74,172,250,110.35,62,250,68.93,70,71,49.02,52,57,107.18,87,250,68.49,69,70,64.78,66,68,81.66,51,250,55.34,56,2,156.6,217,250,64.01,65,66,108.82,98,250,66.77,66,67,55.48,22,2,67.99,34,5,103.89,81,250,42.08,24,8,64.5,66,67,66.19,39,22,155.44,205,250,63.78,65,65,72.78,45,26,79.69,70,60,62.26,64,64,84.04,92,111,40.09,39,41,65.04,64,66,63.32,65,67,91.09,46,250,59.54,63,65,51.26,57,60,66.48,66,67,76.25,68,3,71.95,72,72,63.73,65,66,64.14,66,66,118.78,133,250,63.57,64,65,62.81,63,63,63.04,62,64,67.24,49,9,127.05,80,250,67.87,68,68,63.54,57,2,75.09,75,75,64.85,66,67,63.6,64,65,43.79,26,20,76.16,76,77,63.35,65,66,66.42,66,65,64.26,66,67,60.81,61,63,68.7,65,66,53.9,59,73,70.35,72,73,224.92,250,250,59.38,61,61,65.13,66,65,57.38,60,62,66.77,67,65,8.65,8,2,67.49,67,67,68.14,69,70,63.09,64,64,61.1,62,63,62.27,61,64,96.13,57,250,63.5,62,64,62.54,65,66,60.86,58,67,61.54,61,61,63.49,66,66,102.13,51,250,68.92,70,70,66.66,61,250,65.08,66,69,71.27,68,71,62.52,65,66,64.6,60,62,59.9,59,64,75.53,40,250,62.05,63,64,57.54,60,64,65.36,64,64,71.06,71,72,61.4,60,60,109.43,91,250,71.67,53,250,99.26,80,250,50.38,44,3,67.51,59,250,76.06,77,77,60.36,60,63,95.24,43,250,99.46,101,106,65.53,67,68,78.18,45,250,65.27,44,250,67.97,68,71,76.84,57,250,67.29,42,250,63.29,41,2,55.16,56,60,64.28,61,61,100.91,63,250,61.17,59,56,66.77,68,69,76.12,56,250,97.93,72,250,64.74,65,66,83.71,39,250,134.24,133,250,75.81,49,250,65.09,60,62,45.6,36,5,51.95,51,60,122.8,131,250,0.948,0.03438 diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv new file mode 100644 index 000000000..d7514da1a --- /dev/null +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv @@ -0,0 +1,48 @@ +sample_id,run_ena +VBS46299-6321STDY9453299,"ERR5967855, ERR5967879, ERR5967903" +VBS46300-6321STDY9453300,"ERR5967861, ERR5967885, ERR5967909" +VBS46301-6321STDY9453301,"ERR5967867, ERR5967891, ERR5967915" +VBS46302-6321STDY9453302,"ERR5967873, ERR5967897, ERR5967921" +VBS46303-6321STDY9453303,"ERR6045486, ERR6045509, ERR6045532" +VBS46304-6321STDY9453304,"ERR6045492, ERR6045515, ERR6045538" +VBS46305-6321STDY9453305,"ERR6045498, ERR6045521, ERR6045544" +VBS46306-6321STDY9453306,"ERR6045504, ERR6045527, ERR6045550" +VBS46307-6321STDY9453307,"ERR5967856, ERR5967880, ERR5967904" +VBS46308-6321STDY9453308,"ERR5967862, ERR5967886, ERR5967910" +VBS46309-6321STDY9453309,"ERR5967868, ERR5967892, ERR5967916" +VBS46310-6321STDY9453310,"ERR5967874, ERR5967898, ERR5967922" +VBS46311-6321STDY9453311,"ERR6045487, ERR6045510, ERR6045533" +VBS46312-6321STDY9453312,"ERR6045493, ERR6045516, ERR6045539" +VBS46313-6321STDY9453313,"ERR6045499, ERR6045522, ERR6045545" +VBS46314-6321STDY9453314,"ERR6045505, ERR6045528, ERR6045551" +VBS46315-6321STDY9453315,"ERR5967857, ERR5967881, ERR5967905" +VBS46316-6321STDY9453316,"ERR5967863, ERR5967887, ERR5967911" +VBS46317-6321STDY9453317,"ERR5967869, ERR5967893, ERR5967917" +VBS46318-6321STDY9453318,"ERR5967875, ERR5967899, ERR5967923" +VBS46319-6321STDY9453319,"ERR6045488, ERR6045511, ERR6045534" +VBS46320-6321STDY9453320,"ERR6045494, ERR6045517, ERR6045540" +VBS46321-6321STDY9453321,"ERR6045500, ERR6045523, ERR6045546" +VBS46322-6321STDY9453322,"ERR6045506, ERR6045529, ERR6045552" +VBS46323-6321STDY9453323,"ERR5967858, ERR5967882, ERR5967906" +VBS46324-6321STDY9453324,"ERR5967864, ERR5967888, ERR5967912" +VBS46325-6321STDY9453325,"ERR5967870, ERR5967894, ERR5967918" +VBS46326-6321STDY9453326,"ERR5967876, ERR5967900, ERR5967924" +VBS46327-6321STDY9453327,"ERR6045489, ERR6045512, ERR6045535" +VBS46328-6321STDY9453328,"ERR6045495, ERR6045518, ERR6045541" +VBS46329-6321STDY9453329,"ERR6045501, ERR6045524, ERR6045547" +VBS46330-6321STDY9453330,"ERR6045507, ERR6045530, ERR6045553" +VBS46331-6321STDY9453331,"ERR5967859, ERR5967883, ERR5967907" +VBS46332-6321STDY9453332,"ERR5967865, ERR5967889, ERR5967913" +VBS46333-6321STDY9453333,"ERR5967871, ERR5967895, ERR5967919" +VBS46334-6321STDY9453334,"ERR5967877, ERR5967901, ERR5967925" +VBS46335-6321STDY9453335,"ERR6045490, ERR6045513, ERR6045536" +VBS46336-6321STDY9453336,"ERR6045496, ERR6045519, ERR6045542" +VBS46337-6321STDY9453337,"ERR6045502, ERR6045525, ERR6045548" +VBS46338-6321STDY9453338,"ERR6045508, ERR6045531, ERR6045554" +VBS46339-6321STDY9453339,"ERR5967860, ERR5967884, ERR5967908" +VBS46340-6321STDY9453340,"ERR5967866, ERR5967890, ERR5967914" +VBS46341-6321STDY9453341,"ERR5967872, ERR5967896, ERR5967920" +VBS46342-6321STDY9453342,"ERR5967878, ERR5967902, ERR5967926" +VBS46343-6321STDY9453343,"ERR6045491, ERR6045514, ERR6045537" +VBS46344-6321STDY9453344,"ERR6045497, ERR6045520, ERR6045543" +VBS46345-6321STDY9453345,"ERR6045503, ERR6045526, ERR6045549" diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/samples.meta.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/samples.meta.csv index 0fa8ea5c8..0881518fe 100644 --- a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/samples.meta.csv +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/samples.meta.csv @@ -1,27 +1,27 @@ -sample_id,derived_sample_id,partner_sample_id,contributor,country,location,year,month,latitude,longitude -VBS45687-6143STDY8787412,VBS45687-6143STDY8787412,A2682,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45688-6143STDY8787413,VBS45688-6143STDY8787413,A2685,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45689-6143STDY8787414,VBS45689-6143STDY8787414,A2686,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45690-6143STDY8787415,VBS45690-6143STDY8787415,A2688,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45691-6143STDY8787416,VBS45691-6143STDY8787416,A2631,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45692-6143STDY8787417,VBS45692-6143STDY8787417,A2645,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45701-6143STDY8787420,VBS45701-6143STDY8787420,A2675,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45702-6143STDY8787421,VBS45702-6143STDY8787421,A2749,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45708-6143STDY8787424,VBS45708-6143STDY8787424,A2709,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45709-6143STDY8787425,VBS45709-6143STDY8787425,A2710,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45711-6143STDY8787426,VBS45711-6143STDY8787426,A2718,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45713-6143STDY8787427,VBS45713-6143STDY8787427,A2722,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997 -VBS45717-6143STDY8787429,VBS45717-6143STDY8787429,A4003,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45718-6143STDY8787430,VBS45718-6143STDY8787430,A4004,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45720-6143STDY8787431,VBS45720-6143STDY8787431,A3930,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45723-6143STDY8787432,VBS45723-6143STDY8787432,A3956,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45724-6143STDY8787433,VBS45724-6143STDY8787433,A3964,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45728-6143STDY8787434,VBS45728-6143STDY8787434,A3988,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45734-6143STDY8787435,VBS45734-6143STDY8787435,A3925,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45735-6143STDY8787436,VBS45735-6143STDY8787436,A3926,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45737-6143STDY8787437,VBS45737-6143STDY8787437,A4007,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45738-6143STDY8787438,VBS45738-6143STDY8787438,A4008,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45739-6143STDY8787439,VBS45739-6143STDY8787439,A4009,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45742-6143STDY8787440,VBS45742-6143STDY8787440,A4013,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45743-6143STDY8787441,VBS45743-6143STDY8787441,A4014,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 -VBS45745-6143STDY8787442,VBS45745-6143STDY8787442,A4019,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093 +sample_id,partner_sample_id,contributor,country,location,year,month,latitude,longitude,sex_call +VBS45687-6143STDY8787412,A2682,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45688-6143STDY8787413,A2685,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45689-6143STDY8787414,A2686,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45690-6143STDY8787415,A2688,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45691-6143STDY8787416,A2631,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45692-6143STDY8787417,A2645,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45701-6143STDY8787420,A2675,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45702-6143STDY8787421,A2749,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45708-6143STDY8787424,A2709,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45709-6143STDY8787425,A2710,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45711-6143STDY8787426,A2718,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45713-6143STDY8787427,A2722,Amelie Vantaux,Cambodia,Deep forest_3,2017,8,12.287,106.997,UKN +VBS45717-6143STDY8787429,A4003,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45718-6143STDY8787430,A4004,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45720-6143STDY8787431,A3930,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45723-6143STDY8787432,A3956,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45724-6143STDY8787433,A3964,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45728-6143STDY8787434,A3988,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45734-6143STDY8787435,A3925,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45735-6143STDY8787436,A3926,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45737-6143STDY8787437,A4007,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45738-6143STDY8787438,A4008,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45739-6143STDY8787439,A4009,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45742-6143STDY8787440,A4013,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45743-6143STDY8787441,A4014,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN +VBS45745-6143STDY8787442,A4019,Amelie Vantaux,Cambodia,Deep forest_4,2018,1,12.326,107.093,UKN diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv index fa5b7c3ea..c5514f4cc 100644 --- a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv @@ -1,27 +1,27 @@ -,sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence -0,VBS45687-6143STDY8787412,32.18,32,32,32.03,32,32,32.37,32,32,32.26,32,32,32.16,32,32,32.07,32,31,0.983,0.01374 -1,VBS45688-6143STDY8787413,33.19,33,33,33.0,33,33,33.35,33,33,33.27,33,33,33.24,33,33,33.14,33,33,0.984,0.01378 -2,VBS45689-6143STDY8787414,34.26,34,34,34.05,34,34,34.53,34,34,34.29,34,34,34.26,34,34,34.19,34,33,0.984,0.01378 -3,VBS45690-6143STDY8787415,33.07,33,33,32.91,33,33,33.32,33,33,33.19,33,33,33.0,33,33,32.89,33,33,0.984,0.01377 -4,VBS45691-6143STDY8787416,34.81,35,34,34.77,35,34,35.02,35,34,35.07,35,35,34.36,34,35,34.7,35,35,0.984,0.01377 -5,VBS45692-6143STDY8787417,31.07,31,31,30.85,31,31,31.24,31,31,31.11,31,31,31.13,31,31,31.14,31,31,0.983,0.01377 -8,VBS45701-6143STDY8787420,9.96,9,9,9.91,9,9,10.07,9,9,9.94,9,9,9.91,9,9,9.96,9,9,0.981,0.01546 -9,VBS45702-6143STDY8787421,8.77,8,8,8.76,8,8,8.81,8,8,8.85,8,8,8.67,8,8,8.74,8,8,0.981,0.01543 -12,VBS45708-6143STDY8787424,10.22,10,9,10.23,10,9,10.32,10,9,10.38,10,9,9.9,9,9,10.19,10,9,0.981,0.01538 -13,VBS45709-6143STDY8787425,8.32,8,7,8.31,8,7,8.43,8,7,8.4,8,7,8.1,7,7,8.29,8,7,0.98,0.01539 -14,VBS45711-6143STDY8787426,9.93,9,9,9.94,9,9,10.05,9,9,10.06,9,9,9.62,9,9,9.88,9,9,0.982,0.01536 -15,VBS45713-6143STDY8787427,23.63,23,23,23.54,23,23,23.78,23,23,23.77,23,23,23.41,23,23,23.64,23,23,0.983,0.01382 -17,VBS45717-6143STDY8787429,34.14,34,34,33.83,34,34,34.26,34,34,34.18,34,34,34.39,34,34,34.19,34,34,0.984,0.01375 -18,VBS45718-6143STDY8787430,35.17,35,35,34.87,35,35,35.34,35,35,35.21,35,35,35.29,35,35,35.26,35,35,0.984,0.01387 -19,VBS45720-6143STDY8787431,38.61,38,38,38.39,38,38,38.81,39,38,38.61,39,38,38.61,39,38,38.71,39,39,0.984,0.0138 -20,VBS45723-6143STDY8787432,39.79,40,40,39.73,40,40,40.05,40,40,40.21,40,40,39.09,39,39,39.73,40,40,0.984,0.01373 -21,VBS45724-6143STDY8787433,34.51,34,34,34.28,34,34,34.63,34,34,34.74,35,34,34.46,34,34,34.51,34,34,0.984,0.01378 -22,VBS45728-6143STDY8787434,49.49,49,49,49.16,49,49,49.6,49,49,49.69,50,50,49.47,50,50,49.73,50,49,0.984,0.0138 -23,VBS45734-6143STDY8787435,33.45,33,33,33.27,33,33,33.67,33,33,33.43,33,33,33.65,33,33,33.23,33,33,0.984,0.01379 -24,VBS45735-6143STDY8787436,33.51,33,33,33.25,33,33,33.58,33,33,33.75,34,33,33.47,33,33,33.7,34,33,0.984,0.01378 -25,VBS45737-6143STDY8787437,38.95,39,39,38.77,39,38,39.12,39,39,39.23,39,39,38.87,39,39,38.77,39,38,0.984,0.01379 -26,VBS45738-6143STDY8787438,39.63,40,39,39.44,39,39,39.84,40,39,39.87,40,39,39.46,39,39,39.57,39,39,0.984,0.01378 -27,VBS45739-6143STDY8787439,38.75,39,38,38.43,38,38,39.04,39,39,38.71,39,38,39.04,39,39,38.59,38,38,0.984,0.01376 -28,VBS45742-6143STDY8787440,43.47,43,43,43.37,43,44,43.52,43,43,43.55,43,43,43.32,43,43,43.61,43,43,0.984,0.01376 -29,VBS45743-6143STDY8787441,41.01,41,41,41.0,41,41,41.3,41,41,41.51,41,41,40.23,40,40,40.81,41,41,0.984,0.01376 -30,VBS45745-6143STDY8787442,46.48,46,46,46.58,46,46,46.9,46,46,47.01,47,46,45.45,45,45,46.04,46,46,0.984,0.01381 +sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence +VBS45687-6143STDY8787412,32.18,32,32,32.03,32,32,32.37,32,32,32.26,32,32,32.16,32,32,32.07,32,31,0.983,0.01374 +VBS45688-6143STDY8787413,33.19,33,33,33,33,33,33.35,33,33,33.27,33,33,33.24,33,33,33.14,33,33,0.984,0.01378 +VBS45689-6143STDY8787414,34.26,34,34,34.05,34,34,34.53,34,34,34.29,34,34,34.26,34,34,34.19,34,33,0.984,0.01378 +VBS45690-6143STDY8787415,33.07,33,33,32.91,33,33,33.32,33,33,33.19,33,33,33,33,33,32.89,33,33,0.984,0.01377 +VBS45691-6143STDY8787416,34.81,35,34,34.77,35,34,35.02,35,34,35.07,35,35,34.36,34,35,34.7,35,35,0.984,0.01377 +VBS45692-6143STDY8787417,31.07,31,31,30.85,31,31,31.24,31,31,31.11,31,31,31.13,31,31,31.14,31,31,0.983,0.01377 +VBS45701-6143STDY8787420,9.96,9,9,9.91,9,9,10.07,9,9,9.94,9,9,9.91,9,9,9.96,9,9,0.981,0.01546 +VBS45702-6143STDY8787421,8.77,8,8,8.76,8,8,8.81,8,8,8.85,8,8,8.67,8,8,8.74,8,8,0.981,0.01543 +VBS45708-6143STDY8787424,10.22,10,9,10.23,10,9,10.32,10,9,10.38,10,9,9.9,9,9,10.19,10,9,0.981,0.01538 +VBS45709-6143STDY8787425,8.32,8,7,8.31,8,7,8.43,8,7,8.4,8,7,8.1,7,7,8.29,8,7,0.98,0.01539 +VBS45711-6143STDY8787426,9.93,9,9,9.94,9,9,10.05,9,9,10.06,9,9,9.62,9,9,9.88,9,9,0.982,0.01536 +VBS45713-6143STDY8787427,23.63,23,23,23.54,23,23,23.78,23,23,23.77,23,23,23.41,23,23,23.64,23,23,0.983,0.01382 +VBS45717-6143STDY8787429,34.14,34,34,33.83,34,34,34.26,34,34,34.18,34,34,34.39,34,34,34.19,34,34,0.984,0.01375 +VBS45718-6143STDY8787430,35.17,35,35,34.87,35,35,35.34,35,35,35.21,35,35,35.29,35,35,35.26,35,35,0.984,0.01387 +VBS45720-6143STDY8787431,38.61,38,38,38.39,38,38,38.81,39,38,38.61,39,38,38.61,39,38,38.71,39,39,0.984,0.0138 +VBS45723-6143STDY8787432,39.79,40,40,39.73,40,40,40.05,40,40,40.21,40,40,39.09,39,39,39.73,40,40,0.984,0.01373 +VBS45724-6143STDY8787433,34.51,34,34,34.28,34,34,34.63,34,34,34.74,35,34,34.46,34,34,34.51,34,34,0.984,0.01378 +VBS45728-6143STDY8787434,49.49,49,49,49.16,49,49,49.6,49,49,49.69,50,50,49.47,50,50,49.73,50,49,0.984,0.0138 +VBS45734-6143STDY8787435,33.45,33,33,33.27,33,33,33.67,33,33,33.43,33,33,33.65,33,33,33.23,33,33,0.984,0.01379 +VBS45735-6143STDY8787436,33.51,33,33,33.25,33,33,33.58,33,33,33.75,34,33,33.47,33,33,33.7,34,33,0.984,0.01378 +VBS45737-6143STDY8787437,38.95,39,39,38.77,39,38,39.12,39,39,39.23,39,39,38.87,39,39,38.77,39,38,0.984,0.01379 +VBS45738-6143STDY8787438,39.63,40,39,39.44,39,39,39.84,40,39,39.87,40,39,39.46,39,39,39.57,39,39,0.984,0.01378 +VBS45739-6143STDY8787439,38.75,39,38,38.43,38,38,39.04,39,39,38.71,39,38,39.04,39,39,38.59,38,38,0.984,0.01376 +VBS45742-6143STDY8787440,43.47,43,43,43.37,43,44,43.52,43,43,43.55,43,43,43.32,43,43,43.61,43,43,0.984,0.01376 +VBS45743-6143STDY8787441,41.01,41,41,41,41,41,41.3,41,41,41.51,41,41,40.23,40,40,40.81,41,41,0.984,0.01376 +VBS45745-6143STDY8787442,46.48,46,46,46.58,46,46,46.9,46,46,47.01,47,46,45.45,45,45,46.04,46,46,0.984,0.01381 diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv new file mode 100644 index 000000000..5beda0a88 --- /dev/null +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv @@ -0,0 +1,27 @@ +sample_id,run_ena +VBS45687-6143STDY8787412,"ERR4696346, ERR4766075, ERR4766106" +VBS45688-6143STDY8787413,"ERR4696347, ERR4766076, ERR4766107" +VBS45689-6143STDY8787414,"ERR4696348, ERR4766077, ERR4766108" +VBS45690-6143STDY8787415,"ERR4696349, ERR4766078, ERR4766109" +VBS45691-6143STDY8787416,"ERR4696350, ERR4766079, ERR4766110" +VBS45692-6143STDY8787417,"ERR4696351, ERR4766080, ERR4766111" +VBS45701-6143STDY8787420,"ERR4696354, ERR4766083, ERR4766114" +VBS45702-6143STDY8787421,"ERR4696355, ERR4766084, ERR4766115" +VBS45708-6143STDY8787424,"ERR4696358, ERR4766087, ERR4766118" +VBS45709-6143STDY8787425,"ERR4696359, ERR4766088, ERR4766119" +VBS45711-6143STDY8787426,"ERR4696360, ERR4766089, ERR4766120" +VBS45713-6143STDY8787427,"ERR4696361, ERR4766090, ERR4766121" +VBS45717-6143STDY8787429,"ERR4696363, ERR4766092, ERR4766123" +VBS45718-6143STDY8787430,"ERR4696364, ERR4766093, ERR4766124" +VBS45720-6143STDY8787431,"ERR4696365, ERR4766094, ERR4766125" +VBS45723-6143STDY8787432,"ERR4696366, ERR4766095, ERR4766126" +VBS45724-6143STDY8787433,"ERR4696367, ERR4766096, ERR4766127" +VBS45728-6143STDY8787434,"ERR4696368, ERR4766097, ERR4766128" +VBS45734-6143STDY8787435,"ERR4696369, ERR4766098, ERR4766129" +VBS45735-6143STDY8787436,"ERR4696370, ERR4766099, ERR4766130" +VBS45737-6143STDY8787437,"ERR4696371, ERR4766100, ERR4766131" +VBS45738-6143STDY8787438,"ERR4696372, ERR4766101, ERR4766132" +VBS45739-6143STDY8787439,"ERR4696373, ERR4766102, ERR4766133" +VBS45742-6143STDY8787440,"ERR4696374, ERR4766103, ERR4766134" +VBS45743-6143STDY8787441,"ERR4696375, ERR4766104, ERR4766135" +VBS45745-6143STDY8787442,"ERR4696376, ERR4766105, ERR4766136" diff --git a/tests/anoph/test_base.py b/tests/anoph/test_base.py index 8d7e22499..0eab7f853 100644 --- a/tests/anoph/test_base.py +++ b/tests/anoph/test_base.py @@ -6,6 +6,7 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.base import AnophelesBase @@ -33,6 +34,18 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesBase( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for @@ -53,6 +66,10 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api + + @parametrize_with_cases("fixture,api", cases=".") def test_config(fixture, api): config = api.config diff --git a/tests/anoph/test_dipclust.py b/tests/anoph/test_dipclust.py index c0bbad033..72e003b94 100644 --- a/tests/anoph/test_dipclust.py +++ b/tests/anoph/test_dipclust.py @@ -4,6 +4,7 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.dipclust import AnophelesDipClustAnalysis @@ -60,6 +61,24 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesDipClustAnalysis( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + default_site_mask="dirus", + results_cache=adir1_sim_fixture.results_cache_path.as_posix(), + taxon_colors=_adir1.TAXON_COLORS, + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for @@ -80,6 +99,10 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api + + @pytest.mark.parametrize("distance_metric", ["cityblock", "euclidean"]) @parametrize_with_cases("fixture,api", cases=".") def test_plot_diplotype_clustering( diff --git a/tests/anoph/test_distance.py b/tests/anoph/test_distance.py index 9091ee454..9565580e4 100644 --- a/tests/anoph/test_distance.py +++ b/tests/anoph/test_distance.py @@ -7,6 +7,7 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.distance import AnophelesDistanceAnalysis from malariagen_data.anoph import pca_params @@ -56,6 +57,24 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesDistanceAnalysis( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + default_site_mask="dirus", + results_cache=adir1_sim_fixture.results_cache_path.as_posix(), + taxon_colors=_adir1.TAXON_COLORS, + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for @@ -76,6 +95,10 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api + + def check_biallelic_diplotype_pairwise_distance(*, api, data_params, metric): # Check available data. ds = api.biallelic_snp_calls(**data_params) diff --git a/tests/anoph/test_fst.py b/tests/anoph/test_fst.py index 098f08538..8cfaea808 100644 --- a/tests/anoph/test_fst.py +++ b/tests/anoph/test_fst.py @@ -9,6 +9,7 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.fst import AnophelesFstAnalysis @@ -57,6 +58,24 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesFstAnalysis( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + default_site_mask="dirus", + results_cache=adir1_sim_fixture.results_cache_path.as_posix(), + taxon_colors=_adir1.TAXON_COLORS, + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for @@ -77,6 +96,10 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api + + @parametrize_with_cases("fixture,api", cases=".") def test_fst_gwss(fixture, api: AnophelesFstAnalysis): # Set up test parameters. diff --git a/tests/anoph/test_g123.py b/tests/anoph/test_g123.py index ab5e25537..6ab324d1d 100644 --- a/tests/anoph/test_g123.py +++ b/tests/anoph/test_g123.py @@ -6,6 +6,7 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.g123 import AnophelesG123Analysis @@ -56,6 +57,25 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesG123Analysis( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + default_site_mask="dirus", + results_cache=adir1_sim_fixture.results_cache_path.as_posix(), + taxon_colors=_adir1.TAXON_COLORS, + default_phasing_analysis="dirus_noneyet", + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for @@ -76,6 +96,10 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api + + def check_g123_gwss(*, api, g123_params): # Run main gwss function under test. x, g123 = api.g123_gwss(**g123_params) diff --git a/tests/anoph/test_genome_features.py b/tests/anoph/test_genome_features.py index eaef4ee4e..1bceb6d37 100644 --- a/tests/anoph/test_genome_features.py +++ b/tests/anoph/test_genome_features.py @@ -7,6 +7,7 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.genome_features import AnophelesGenomeFeaturesData from malariagen_data.util import Region, resolve_region @@ -42,6 +43,21 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesGenomeFeaturesData( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + ) + + def case_ag3_sim(ag3_sim_fixture, ag3_sim_api): return ag3_sim_fixture, ag3_sim_api @@ -50,6 +66,10 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api + + gff3_cols = [ "contig", "source", @@ -91,6 +111,15 @@ def test_genome_features_default_attributes_af1( assert df_gf.columns.to_list() == expected_cols +def test_genome_features_default_attributes_adir1( + adir1_sim_api: AnophelesGenomeFeaturesData, +): + df_gf = adir1_sim_api.genome_features() + assert isinstance(df_gf, pd.DataFrame) + expected_cols = gff3_cols + ["ID", "Parent", "Note", "description"] + assert df_gf.columns.to_list() == expected_cols + + @parametrize_with_cases("fixture,api", cases=".") def test_genome_features_region_contig(fixture, api: AnophelesGenomeFeaturesData): for contig in fixture.contigs: diff --git a/tests/anoph/test_pca.py b/tests/anoph/test_pca.py index e5fa667a6..6ca02bf03 100644 --- a/tests/anoph/test_pca.py +++ b/tests/anoph/test_pca.py @@ -8,6 +8,7 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.pca import AnophelesPca from malariagen_data.anoph import pca_params @@ -57,6 +58,24 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesPca( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + default_site_mask="dirus", + results_cache=adir1_sim_fixture.results_cache_path.as_posix(), + taxon_colors=_adir1.TAXON_COLORS, + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for @@ -77,6 +96,10 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api + + @parametrize_with_cases("fixture,api", cases=".") def test_pca_plotting(fixture, api: AnophelesPca): # Parameters for selecting input data. diff --git a/tests/anoph/test_plink_converter.py b/tests/anoph/test_plink_converter.py index 44e476cd9..0480670ca 100644 --- a/tests/anoph/test_plink_converter.py +++ b/tests/anoph/test_plink_converter.py @@ -4,6 +4,8 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 + from malariagen_data.anoph.to_plink import PlinkConverter import os @@ -57,6 +59,24 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return PlinkConverter( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + default_site_mask="dirus", + results_cache=adir1_sim_fixture.results_cache_path.as_posix(), + taxon_colors=_adir1.TAXON_COLORS, + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for diff --git a/tests/anoph/test_sample_metadata.py b/tests/anoph/test_sample_metadata.py index 68d51c6ff..935e3bdb9 100644 --- a/tests/anoph/test_sample_metadata.py +++ b/tests/anoph/test_sample_metadata.py @@ -13,7 +13,6 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 from malariagen_data import adir1 as _adir1 -from malariagen_data import amin1 as _amin1 from malariagen_data.anoph.sample_metadata import AnophelesSampleMetadata @@ -65,19 +64,6 @@ def adir1_sim_api(adir1_sim_fixture): ) -@pytest.fixture -def amin1_sim_api(amin1_sim_fixture): - return AnophelesSampleMetadata( - url=amin1_sim_fixture.url, - public_url=amin1_sim_fixture.url, - config_path=_amin1.CONFIG_PATH, - major_version_number=_amin1.MAJOR_VERSION_NUMBER, - major_version_path=_amin1.MAJOR_VERSION_PATH, - pre=False, - taxon_colors=_amin1.TAXON_COLORS, - ) - - @pytest.fixture def missing_metadata_api(fixture_dir): # In this fixture, one of the sample sets (AG1000G-BF-A) has missing files @@ -108,12 +94,8 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api -def case_adir1_sim(adir1_sim_fixture, adir_sim_api): - return adir1_sim_fixture, adir_sim_api - - -def case_amin1_sim(amin1_sim_fixture, amin1_sim_api): - return amin1_sim_fixture, amin1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api def general_metadata_expected_columns(): diff --git a/tests/anoph/test_snp_frq.py b/tests/anoph/test_snp_frq.py index f7a0224f6..ccb85917c 100644 --- a/tests/anoph/test_snp_frq.py +++ b/tests/anoph/test_snp_frq.py @@ -10,6 +10,8 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 + from malariagen_data.anoph.snp_frq import AnophelesSnpFrequencyAnalysis from malariagen_data.util import compare_series_like from .test_frq import ( @@ -66,6 +68,24 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesSnpFrequencyAnalysis( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + default_site_mask="dirus", + results_cache=adir1_sim_fixture.results_cache_path.as_posix(), + taxon_colors=_adir1.TAXON_COLORS, + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for @@ -86,6 +106,10 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): + return adir1_sim_fixture, adir1_sim_api + + expected_alleles = list("ACGT") expected_effects = [ "FIVE_PRIME_UTR", From 7303340b9479aa28872fdc544989ac976fc06061 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 25 Nov 2025 11:24:36 +1000 Subject: [PATCH 35/41] fix cohort validation in adir1 conftest & add dummy contam data --- .../samples.admin_units.csv | 48 ++ .../samples.cohorts.csv | 48 ++ .../1276-AD-BD-ALAM-VMF00156/samples.taxa.csv | 48 ++ .../samples.admin_units.csv | 27 + .../samples.cohorts.csv | 27 + .../samples.taxa.csv | 27 + .../samples.admin_units.csv | 249 +++++++++ .../samples.cohorts.csv | 249 +++++++++ .../samples.taxa.csv | 249 +++++++++ .../samples.admin_units.csv | 220 ++++++++ .../samples.cohorts.csv | 220 ++++++++ .../samples.taxa.csv | 220 ++++++++ .../sequence_qc_stats.csv | 48 ++ .../sequence_qc_stats.csv | 27 + .../sequence_qc_stats.csv | 249 +++++++++ .../sequence_qc_stats.csv | 220 ++++++++ .../1276-AD-BD-ALAM-VMF00156/samples.meta.csv | 48 ++ .../sequence_qc_stats.csv | 48 ++ .../wgs_accession_data.csv | 48 ++ .../1276-AD-BD-ALAM-VMF00156/wgs_snp_data.csv | 48 ++ .../samples.meta.csv | 27 + .../sequence_qc_stats.csv | 27 + .../wgs_accession_data.csv | 27 + .../wgs_snp_data.csv | 27 + .../samples.meta.csv | 249 +++++++++ .../sequence_qc_stats.csv | 249 +++++++++ .../wgs_accession_data.csv | 249 +++++++++ .../wgs_snp_data.csv | 249 +++++++++ .../samples.meta.csv | 220 ++++++++ .../sequence_qc_stats.csv | 220 ++++++++ .../wgs_accession_data.csv | 220 ++++++++ .../wgs_snp_data.csv | 220 ++++++++ tests/anoph/conftest.py | 2 +- .../sequence_qc_stats.csv | 96 ++-- .../sequence_qc_stats.csv | 54 +- .../sequence_qc_stats.csv | 498 +++++++++--------- .../sequence_qc_stats.csv | 440 ++++++++-------- .../1175-VO-KH-STLAURENT/samples.meta.csv | 303 +++++++++++ .../sequence_qc_stats.csv | 303 +++++++++++ .../1175-VO-KH-STLAURENT/wgs_snp_data.csv | 303 +++++++++++ .../1276-AD-BD-ALAM-VMF00156/samples.meta.csv | 94 ++-- .../sequence_qc_stats.csv | 96 ++-- .../wgs_accession_data.csv | 96 ++-- .../sequence_qc_stats.csv | 52 +- .../wgs_accession_data.csv | 54 +- .../samples.meta.csv | 249 +++++++++ .../sequence_qc_stats.csv | 249 +++++++++ .../wgs_accession_data.csv | 249 +++++++++ .../wgs_snp_data.csv | 249 +++++++++ .../samples.meta.csv | 220 ++++++++ .../sequence_qc_stats.csv | 220 ++++++++ .../wgs_accession_data.csv | 220 ++++++++ .../wgs_snp_data.csv | 220 ++++++++ tests/anoph/test_g123.py | 2 +- 54 files changed, 7879 insertions(+), 742 deletions(-) create mode 100644 metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.admin_units.csv create mode 100644 metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.cohorts.csv create mode 100644 metadata/cohorts_20250710/1276-AD-BD-ALAM-VMF00156/samples.taxa.csv create mode 100644 metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.admin_units.csv create mode 100644 metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.cohorts.csv create mode 100644 metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00151/samples.taxa.csv create mode 100644 metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00183/samples.admin_units.csv create mode 100644 metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00183/samples.cohorts.csv create mode 100644 metadata/cohorts_20250710/1277-VO-KH-WITKOWSKI-VMF00183/samples.taxa.csv create mode 100644 metadata/cohorts_20250710/1278-VO-TH-KOBYLINSKI-VMF00153/samples.admin_units.csv create mode 100644 metadata/cohorts_20250710/1278-VO-TH-KOBYLINSKI-VMF00153/samples.cohorts.csv create mode 100644 metadata/cohorts_20250710/1278-VO-TH-KOBYLINSKI-VMF00153/samples.taxa.csv create mode 100644 metadata/curation/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv create mode 100644 metadata/curation/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv create mode 100644 metadata/curation/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv create mode 100644 metadata/curation/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv create mode 100644 metadata/general/1276-AD-BD-ALAM-VMF00156/samples.meta.csv create mode 100644 metadata/general/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv create mode 100644 metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv create mode 100644 metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_snp_data.csv create mode 100644 metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/samples.meta.csv create mode 100644 metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv create mode 100644 metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv create mode 100644 metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_snp_data.csv create mode 100644 metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/samples.meta.csv create mode 100644 metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv create mode 100644 metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/wgs_accession_data.csv create mode 100644 metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/wgs_snp_data.csv create mode 100644 metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/samples.meta.csv create mode 100644 metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv create mode 100644 metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_accession_data.csv create mode 100644 metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/wgs_snp_data.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1175-VO-KH-STLAURENT/samples.meta.csv create mode 100644 tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1175-VO-KH-STLAURENT/sequence_qc_stats.csv create mode 100644 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Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46083-6296STDY9478692,3185,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,UKN +VBS46084-6296STDY9478693,3191,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,UKN +VBS46087-6296STDY9478696,3325,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,UKN +VBS46088-6296STDY9478697,3330,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,UKN +VBS46098-6296STDY9478707,3932_1278,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,3,9.340,98.880,UKN +VBS46121-6296STDY9478730,4591,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46141-6296STDY9478750,5202,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46145-6296STDY9478754,5206,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46146-6296STDY9478755,5209,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46154-6296STDY9478763,5221,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46168-6296STDY9478779,5244,Kevin Kobylinski,Thailand,"Vibhavadi, six, A",2019,10,9.252,98.850,UKN +VBS46172-6296STDY9478782,5265,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,10,9.340,98.880,UKN +VBS46173-6296STDY9478783,5313,Kevin Kobylinski,Thailand,"Vibhavadi, ten, F",2019,10,9.353,98.875,UKN +VBS46175-6296STDY9478785,5496,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46180-6296STDY9478790,5506_1278,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46183-6296STDY9478793,5592,Kevin Kobylinski,Thailand,"Vibhavadi, eight, I",2019,10,9.296,98.886,UKN +VBS46187-6296STDY9478797,5614,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,UKN +VBS46188-6296STDY9478798,5619,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,UKN +VBS46189-6296STDY9478799,5647,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46190-6296STDY9478800,5649,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46192-6296STDY9478801,5683,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, N",2019,10,9.083,98.878,UKN +VBS46198-6296STDY9478807,5736,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS45975-6296STDY10244530,331,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, A",2019,2,9.110,98.878,UKN +VBS45983-6296STDY10244537,1200,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, C1",2019,4,9.080,98.879,UKN +VBS45984-6296STDY10244538,1363,Kevin Kobylinski,Thailand,"Phanom, three, A2",2019,4,8.894,98.667,UKN +VBS45985-6296STDY10244539,1364,Kevin Kobylinski,Thailand,"Phanom, three, A2",2019,4,8.894,98.667,UKN +VBS45986-6296STDY10244540,1494,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, D1",2019,4,9.107,98.869,UKN +VBS45987-6296STDY10244541,1498,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, D2",2019,4,9.107,98.869,UKN +VBS45988-6296STDY10244542,1687,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45989-6296STDY10244543,1688,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45991-6296STDY10244545,1711,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS45992-6296STDY10244546,1719,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45993-6296STDY10244547,1738,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45994-6296STDY10244548,1750,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45995-6296STDY10244549,1759,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45996-6296STDY10244550,1771,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45997-6296STDY10244551,1774,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45998-6296STDY10244552,1780,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS45999-6296STDY10244553,1793,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46000-6296STDY10244554,1810,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46001-6296STDY10244555,1818,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46002-6296STDY10244556,1826_1278,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46003-6296STDY10244557,1830,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46004-6296STDY10244558,1840,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46006-6296STDY10244560,1854,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46007-6296STDY10244561,1859,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46008-6296STDY10244562,1860,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46009-6296STDY10244563,1866,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46010-6296STDY10244564,1871,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46011-6296STDY10244565,1872,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46012-6296STDY10244566,1875,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46013-6296STDY10244567,1881,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46014-6296STDY10244568,1887,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46016-6296STDY10244570,1908,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46017-6296STDY10244571,1912,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46019-6296STDY10244573,1931,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46020-6296STDY10244574,1932,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46021-6296STDY10244575,1934,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46022-6296STDY10244576,1936,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46025-6296STDY10244579,1946,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46026-6296STDY10244580,1949,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46027-6296STDY10244581,1950,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46028-6296STDY10244582,1951,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46029-6296STDY10244583,1954,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46030-6296STDY10244584,1956,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46031-6296STDY10244585,1960,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46032-6296STDY10244586,1966,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46033-6296STDY10244587,1975,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46034-6296STDY10244588,1977,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46035-6296STDY10244589,1978,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46036-6296STDY10244590,1989,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46037-6296STDY10244591,1999,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46038-6296STDY10244592,2000,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46039-6296STDY10244593,2003,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46040-6296STDY10244594,2006,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46041-6296STDY10244595,2011,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46043-6296STDY10244597,2017,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46044-6296STDY10244598,2018,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46045-6296STDY10244599,2028,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46046-6296STDY10244600,2037,Kevin Kobylinski,Thailand,"Phanom, three, B2",2019,5,8.896,98.663,UKN +VBS46047-6296STDY10244601,2039,Kevin Kobylinski,Thailand,"Phanom, three, B2",2019,5,8.896,98.663,UKN +VBS46048-6296STDY10244602,2040,Kevin Kobylinski,Thailand,"Phanom, three, B2",2019,5,8.896,98.663,UKN +VBS46049-6296STDY10244603,2041,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46051-6296STDY10244605,2044,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46052-6296STDY10244606,2045,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46053-6296STDY10244607,2047,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46054-6296STDY10244608,2431,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E1",2019,5,9.068,98.846,UKN +VBS46055-6296STDY10244609,2444,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,UKN +VBS46056-6296STDY10244610,2499,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,UKN +VBS46057-6296STDY10244611,2503,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,UKN +VBS46060-6296STDY10244614,2569,Kevin Kobylinski,Thailand,"Vibhavadi, eleven, A",2019,5,9.360,98.876,UKN +VBS46061-6296STDY10244615,2688,Kevin Kobylinski,Thailand,"Vibhavadi, nine, A3",2019,1,9.331,98.878,UKN +VBS46063-6296STDY10244617,2841,Kevin Kobylinski,Thailand,"Phanom, three, C2",2019,6,8.890,98.663,UKN +VBS46064-6296STDY10244618,2889,Kevin Kobylinski,Thailand,"Phanom, three, C1",2019,6,8.890,98.664,UKN +VBS46065-6296STDY10244619,2894,Kevin Kobylinski,Thailand,"Phanom, three, C1",2019,6,8.890,98.664,UKN +VBS46068-6296STDY10244622,2937,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,UKN +VBS46069-6296STDY10244625,2944,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46070-6296STDY10244626,2960,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46071-6296STDY10244627,2961,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46072-6296STDY10244628,3007,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46073-6296STDY10244629,3037,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, H",2019,6,9.136,98.881,UKN +VBS46074-6296STDY10244630,3041,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, H",2019,6,9.136,98.881,UKN +VBS46075-6296STDY10244631,3062,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46076-6296STDY10244632,3077,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,UKN +VBS46077-6296STDY10244633,3079,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,UKN +VBS46079-6296STDY10244635,3129,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, G",2019,6,9.135,98.882,UKN +VBS46080-6296STDY10244636,3142,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, G",2019,6,9.063,98.877,UKN +VBS46081-6296STDY10244637,3170,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,UKN +VBS46082-6296STDY10244638,3183,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,UKN +VBS46085-6296STDY10244641,3249,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,UKN +VBS46086-6296STDY10244642,3316,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,UKN +VBS46089-6296STDY10244645,3388,Kevin Kobylinski,Thailand,"Vibhavadi, eight, B1",2019,7,9.304,98.885,UKN +VBS46090-6296STDY10244646,3396,Kevin Kobylinski,Thailand,"Vibhavadi, eight, B1",2019,7,9.304,98.885,UKN +VBS46091-6296STDY10244647,3397,Kevin Kobylinski,Thailand,"Vibhavadi, eight, B2",2019,7,9.304,98.886,UKN +VBS46092-6296STDY10244648,3581,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, H",2019,7,9.110,98.880,UKN +VBS46093-6296STDY10244649,3623,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, I",2019,7,9.052,98.865,UKN +VBS46094-6296STDY10244650,3710,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, I",2019,7,9.140,98.881,UKN +VBS46095-6296STDY10244651,3745,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, I",2019,7,9.052,98.865,UKN +VBS46096-6296STDY10244652,3780,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,7,9.082,98.861,UKN +VBS46097-6296STDY10244653,3840,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,3,9.340,98.880,UKN +VBS46099-6296STDY10244655,3954,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,3,9.340,98.880,UKN +VBS46100-6296STDY10244656,4148,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, J",2019,8,9.111,98.881,UKN +VBS46101-6296STDY10244657,4149,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, J",2019,8,9.111,98.881,UKN +VBS46102-6296STDY10244658,4151,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, J",2019,8,9.111,98.881,UKN +VBS46103-6296STDY10244659,4156_1278,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, I",2019,8,9.105,98.889,UKN +VBS46104-6296STDY10244660,4235,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, M",2019,8,9.126,98.903,UKN +VBS46105-6296STDY10244661,4274,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, I",2019,8,9.105,98.889,UKN +VBS46106-6296STDY10244662,4310,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46107-6296STDY10244663,4321,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46108-6296STDY10244664,4407,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, K",2019,8,9.084,98.876,UKN +VBS46109-6296STDY10244665,4430,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, K",2019,8,9.084,98.876,UKN +VBS46110-6296STDY10244666,4472,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, J",2019,8,9.053,98.852,UKN +VBS46111-6296STDY10244667,4488,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, K",2019,8,9.052,98.857,UKN +VBS46112-6296STDY10244668,4511,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, K",2019,8,9.084,98.876,UKN +VBS46113-6296STDY10244669,4556,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46114-6296STDY10244670,4560,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46115-6296STDY10244671,4577,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46116-6296STDY10244672,4578,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46117-6296STDY10244673,4579,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46118-6296STDY10244674,4585,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46119-6296STDY10244675,4589,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46120-6296STDY10244676,4590,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46122-6296STDY10244678,4596,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46123-6296STDY10244679,4609,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46124-6296STDY10244680,4666,Kevin Kobylinski,Thailand,"Vibhavadi, eight, F",2019,2,9.307,98.885,UKN +VBS46125-6296STDY10244681,4768,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46126-6296STDY10244682,4778,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46127-6296STDY10244683,4779,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46128-6296STDY10244684,4788,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46129-6296STDY10244685,4809,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46130-6296STDY10244686,4875,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,2,9.340,98.880,UKN +VBS46131-6296STDY10244687,5191_1278,Kevin Kobylinski,Thailand,"Phanom, one, F",2019,10,8.869,98.638,UKN +VBS46132-6296STDY10244688,5192,Kevin Kobylinski,Thailand,"Phanom, one, F",2019,10,8.869,98.638,UKN +VBS46133-6296STDY10244689,5194,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46134-6296STDY10244690,5195,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46135-6296STDY10244691,5196,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46136-6296STDY10244692,5197,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46137-6296STDY10244693,5198,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46138-6296STDY10244694,5199,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46139-6296STDY10244695,5200,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46140-6296STDY10244696,5201,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46142-6296STDY10244698,5203,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46143-6296STDY10244699,5204,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46144-6296STDY10244700,5205,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46147-6296STDY10244703,5214,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46148-6296STDY10244704,5215,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46149-6296STDY10244705,5216,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46150-6296STDY10244706,5217,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46151-6296STDY10244707,5218,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46152-6296STDY10244708,5219,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46153-6296STDY10244709,5220,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46155-6296STDY10244711,5222,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46156-6296STDY10244712,5223,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46157-6296STDY10244713,5226,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46158-6296STDY10244714,5227,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46160-6296STDY10244716,5230_1278,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46161-6296STDY10244717,5231,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46162-6296STDY10244718,5232,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46163-6296STDY10244721,5233,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46164-6296STDY10244722,5236,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46165-6296STDY10244723,5237,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46166-6296STDY10244724,5238,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46170-6296STDY10244727,5247,Kevin Kobylinski,Thailand,"Vibhavadi, nine, D",2019,10,9.327,98.877,UKN +VBS46171-6296STDY10244728,5248,Kevin Kobylinski,Thailand,"Vibhavadi, nine, D",2019,10,9.327,98.877,UKN +VBS46174-6296STDY10244731,5494,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46176-6296STDY10244733,5500,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46177-6296STDY10244734,5501,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46178-6296STDY10244735,5502,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46179-6296STDY10244736,5505,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46181-6296STDY10244738,5542,Kevin Kobylinski,Thailand,"Vibhavadi, eight, I",2019,10,9.296,98.886,UKN +VBS46182-6296STDY10244739,5548,Kevin Kobylinski,Thailand,"Vibhavadi, eight, I",2019,10,9.296,98.886,UKN +VBS46184-6296STDY10244741,5604,Kevin Kobylinski,Thailand,"Khirirat Nikhom, five, B",2019,10,9.043,98.894,UKN +VBS46185-6296STDY10244742,5609,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,UKN +VBS46186-6296STDY10244743,5613,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,UKN +VBS46193-6296STDY10244749,5697,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, O",2019,10,9.076,98.868,UKN +VBS46194-6296STDY10244750,5721,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46195-6296STDY10244751,5725,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46196-6296STDY10244752,5727,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46197-6296STDY10244753,5728,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46199-6296STDY10244755,5738,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46200-6296STDY10244756,5765,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, K",2019,10,9.108,98.875,UKN +VBS46201-6296STDY10244757,5771,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, K",2019,10,9.108,98.875,UKN +VBS46202-6296STDY10244758,5777,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, L",2019,10,9.109,98.877,UKN +VBS46203-6296STDY10244759,5895,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, Q",2019,10,9.127,98.905,UKN +VBS46204-6296STDY10244760,5972,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, M",2019,10,9.104,98.891,UKN +VBS46205-6296STDY10244761,6024,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, M",2019,10,9.104,98.891,UKN +VBS46206-6296STDY10244762,6036,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, N",2019,10,9.106,98.887,UKN +VBS46207-6296STDY10244763,6037,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, N",2019,10,9.106,98.887,UKN diff --git a/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv b/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv new file mode 100644 index 000000000..41e1c652b --- /dev/null +++ b/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv @@ -0,0 +1,220 @@ +sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence +VBS45974-6296STDY9478582,9.79,9,9,9.79,9,9,9.81,9,9,9.91,10,9,9.81,9,9,9.62,9,9,0.952,0.03652 +VBS45975-6296STDY10244530,75.33,76,75,74.27,74,75,74.89,75,75,76.6,76,75,76.95,78,77,74.97,75,75,0.959,0.03382 +VBS45976-6296STDY9478584,12.9,13,12,12.95,13,12,12.87,13,12,13.16,13,12,12.6,12,12,12.83,13,12,0.952,0.03517 +VBS45979-6296STDY9478587,14.53,14,14,14.56,14,14,14.39,14,14,14.72,14,14,14.56,14,14,14.42,14,14,0.954,0.03525 +VBS45982-6296STDY9478589,20.34,19,18,20.91,20,19,20.46,19,18,20.86,20,18,19.02,18,17,19.81,19,18,0.955,0.03414 +VBS45983-6296STDY10244537,16.39,16,16,16.38,16,16,16.34,16,16,16.93,17,16,16.07,16,16,16.19,16,16,0.955,0.03482 +VBS45984-6296STDY10244538,36.46,37,37,36.39,36,36,36.38,36,37,37.05,37,37,36.14,36,37,36.36,36,37,0.957,0.03366 +VBS45985-6296STDY10244539,37.61,38,38,37.81,38,38,37.37,37,38,38.91,39,38,36.55,37,36,37.22,37,37,0.957,0.03361 +VBS45986-6296STDY10244540,42.12,42,42,42.54,43,42,42.04,42,42,43.8,44,43,40.26,41,41,41.4,42,41,0.956,0.03393 +VBS45987-6296STDY10244541,37.26,37,37,37.56,37,37,37.37,37,37,38.76,39,38,35.6,36,36,36.47,37,36,0.957,0.03383 +VBS45988-6296STDY10244542,38.39,39,39,38.55,39,39,38.36,38,39,39.36,39,39,37.31,38,38,38.11,38,39,0.958,0.03386 +VBS45989-6296STDY10244543,49.81,50,50,49.82,50,50,49.57,50,50,51.36,51,51,48.79,49,49,49.44,50,50,0.957,0.03365 +VBS45991-6296STDY10244545,45.77,46,46,46.01,46,47,45.76,46,46,47.23,47,47,44.29,45,46,45.2,46,46,0.958,0.03387 +VBS45992-6296STDY10244546,37.63,38,38,37.58,38,37,37.6,38,38,38.71,39,38,36.73,37,37,37.43,37,37,0.957,0.03359 +VBS45993-6296STDY10244547,38.07,38,38,38.01,38,38,37.95,38,38,39.0,39,39,37.58,38,38,37.81,38,38,0.957,0.03362 +VBS45994-6296STDY10244548,44.41,45,45,44.32,44,44,44.24,44,44,45.33,45,45,43.8,44,45,44.44,45,45,0.957,0.03363 +VBS45995-6296STDY10244549,38.14,38,38,37.9,38,38,38.13,38,39,39.34,39,39,37.46,38,38,37.94,38,38,0.955,0.03396 +VBS45996-6296STDY10244550,36.73,37,37,36.41,36,36,36.66,37,36,37.77,38,37,36.51,37,37,36.47,37,37,0.957,0.0336 +VBS45997-6296STDY10244551,76.86,78,79,77.22,78,79,76.63,78,79,79.64,80,81,74.05,76,77,76.28,77,78,0.959,0.03383 +VBS45998-6296STDY10244552,64.83,65,66,65.01,65,65,65.03,65,65,66.89,67,67,62.63,64,65,64.1,65,65,0.959,0.03395 +VBS45999-6296STDY10244553,45.76,46,46,45.75,46,46,45.62,46,46,48.71,49,49,43.74,44,45,44.72,45,45,0.958,0.03387 +VBS46000-6296STDY10244554,89.13,90,91,89.65,91,92,88.16,90,90,93.33,94,93,85.9,88,90,88.3,90,89,0.959,0.03382 +VBS46001-6296STDY10244555,35.07,35,35,34.88,35,35,35.04,35,35,36.13,36,36,34.34,34,35,35.01,35,35,0.957,0.03358 +VBS46002-6296STDY10244556,40.42,40,39,40.36,40,38,40.37,40,39,41.57,41,40,39.71,39,38,40.07,39,39,0.957,0.03366 +VBS46003-6296STDY10244557,42.55,42,41,42.5,42,41,42.5,42,41,44.01,44,42,41.62,41,40,41.99,42,41,0.957,0.03363 +VBS46004-6296STDY10244558,42.06,42,42,42.35,42,42,42.17,42,42,44.16,44,44,39.92,40,41,41.1,41,41,0.958,0.03388 +VBS46005-6296STDY9478612,18.82,18,18,18.97,19,18,18.76,18,18,19.12,19,18,18.45,18,17,18.67,18,18,0.955,0.0338 +VBS46006-6296STDY10244560,43.63,44,44,43.5,44,43,43.55,44,44,45.64,46,45,42.36,43,43,43.05,43,43,0.957,0.03363 +VBS46007-6296STDY10244561,39.77,40,40,39.87,40,40,39.84,40,40,40.96,41,40,38.65,39,40,39.24,40,40,0.958,0.03385 +VBS46008-6296STDY10244562,39.04,39,39,39.03,39,39,38.83,39,38,40.34,40,40,38.26,38,39,38.76,39,39,0.957,0.03369 +VBS46009-6296STDY10244563,34.34,34,34,34.29,34,34,34.16,34,34,35.53,35,35,33.61,34,34,34.17,34,34,0.957,0.03363 +VBS46010-6296STDY10244564,44.3,44,44,44.3,44,44,44.4,44,44,45.98,46,45,42.63,43,43,43.95,44,44,0.957,0.03363 +VBS46011-6296STDY10244565,37.81,38,38,37.88,38,38,37.62,38,37,39.19,39,39,36.74,37,37,37.47,37,37,0.958,0.03362 +VBS46012-6296STDY10244566,49.18,49,50,49.36,50,49,49.33,50,50,51.23,51,52,47.19,48,49,48.3,49,49,0.958,0.03389 +VBS46013-6296STDY10244567,49.91,50,51,50.07,50,50,49.97,50,50,51.84,52,52,47.97,49,50,49.29,50,50,0.959,0.03389 +VBS46014-6296STDY10244568,68.98,70,70,68.7,69,70,68.88,69,70,72.02,72,72,67.07,68,69,68.18,69,69,0.958,0.03375 +VBS46016-6296STDY10244570,39.17,39,39,39.29,39,39,39.34,39,39,40.84,41,41,37.47,38,38,38.53,39,39,0.958,0.03383 +VBS46017-6296STDY10244571,36.17,36,36,36.28,36,36,36.03,36,36,37.41,37,37,35.23,35,36,35.76,36,36,0.956,0.03361 +VBS46019-6296STDY10244573,46.77,47,47,46.71,47,47,46.77,47,47,47.71,48,48,45.88,46,47,46.71,47,47,0.957,0.03365 +VBS46020-6296STDY10244574,40.84,41,41,41.04,41,41,40.9,41,41,41.67,42,42,39.73,40,41,40.59,41,41,0.958,0.03382 +VBS46021-6296STDY10244575,42.06,42,42,42.01,42,42,42.02,42,43,43.37,43,43,40.93,41,42,41.86,42,42,0.957,0.03365 +VBS46022-6296STDY10244576,43.49,44,44,43.64,44,44,43.52,44,43,44.97,45,45,42.1,42,43,42.87,43,43,0.956,0.03397 +VBS46025-6296STDY10244579,34.97,35,34,34.7,35,34,35.02,35,34,36.37,36,35,34.05,34,33,34.75,35,34,0.957,0.03357 +VBS46026-6296STDY10244580,39.62,40,40,39.53,40,39,39.44,39,40,41.23,41,41,38.64,39,39,39.29,39,39,0.956,0.03364 +VBS46027-6296STDY10244581,41.05,41,41,41.13,41,41,40.83,41,41,42.48,42,42,40.12,40,40,40.61,41,41,0.956,0.03361 +VBS46028-6296STDY10244582,37.19,37,37,37.45,37,37,37.1,37,37,38.67,38,38,35.89,36,36,36.51,37,36,0.958,0.03385 +VBS46029-6296STDY10244583,28.2,28,28,28.11,28,28,28.11,28,27,28.94,29,28,27.83,28,27,28.06,28,28,0.956,0.03355 +VBS46030-6296STDY10244584,21.85,22,21,21.85,22,21,21.74,22,21,22.7,23,22,21.39,21,21,21.57,21,21,0.955,0.0337 +VBS46031-6296STDY10244585,42.79,43,43,42.82,43,43,42.63,43,43,44.28,44,45,41.68,42,43,42.4,43,42,0.957,0.03365 +VBS46032-6296STDY10244586,33.1,33,32,32.97,33,32,33.08,33,32,33.61,33,33,32.93,33,32,33.0,33,32,0.956,0.03359 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b/tests/anoph/conftest.py index 743191806..b650e5996 100644 --- a/tests/anoph/conftest.py +++ b/tests/anoph/conftest.py @@ -2371,7 +2371,7 @@ def __init__(self, fixture_dir): bucket="vo_adir_release_master_us_central1", releases=("1.0",), has_aims=False, - has_cohorts_by_quarter=False, + has_cohorts_by_quarter=True, has_sequence_qc=True, ) diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv index 8cc1f9da5..817953edc 100644 --- a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1276-AD-BD-ALAM-VMF00156/sequence_qc_stats.csv @@ -1,48 +1,48 @@ -,sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence -0,VBS46299-6321STDY9453299,41.69,42,43,42.02,42,43,41.69,42,42,43.08,43,43,39.73,40,41,41.48,42,42,0.957,0.03433 -1,VBS46300-6321STDY9453300,52.55,53,54,53.0,54,54,52.56,53,54,54.34,55,55,49.91,51,52,52.35,53,53,0.957,0.03436 -2,VBS46301-6321STDY9453301,67.77,69,70,68.26,69,70,67.76,69,69,70.22,71,71,64.45,66,68,67.48,69,70,0.957,0.03442 -3,VBS46302-6321STDY9453302,62.53,63,64,63.09,64,64,62.5,63,64,64.97,65,65,59.1,61,62,62.21,63,64,0.958,0.03441 -4,VBS46303-6321STDY9453303,44.29,45,45,44.67,45,45,44.25,45,45,45.88,46,46,42.03,43,44,44.14,45,45,0.959,0.03424 -5,VBS46304-6321STDY9453304,63.22,64,65,63.72,64,65,63.19,64,65,65.51,66,66,59.98,61,63,63.0,64,65,0.958,0.03448 -6,VBS46305-6321STDY9453305,66.57,68,68,67.22,68,68,66.65,68,67,69.32,70,69,62.55,64,66,66.17,67,68,0.957,0.03441 -7,VBS46306-6321STDY9453306,55.32,56,57,55.87,56,57,55.26,56,57,57.67,58,58,52.19,54,55,54.9,56,57,0.957,0.03434 -8,VBS46307-6321STDY9453307,47.91,48,49,48.35,49,49,47.96,48,49,49.81,50,49,45.08,46,48,47.73,48,49,0.958,0.03415 -9,VBS46308-6321STDY9453308,60.89,62,62,61.42,62,63,60.85,62,62,63.53,64,63,57.36,59,60,60.56,62,62,0.958,0.03438 -10,VBS46309-6321STDY9453309,56.93,58,58,57.43,58,58,56.96,58,58,58.55,59,59,54.33,56,57,56.72,58,58,0.959,0.03429 -11,VBS46310-6321STDY9453310,63.49,64,64,63.85,64,64,63.43,64,65,64.99,65,65,61.5,63,63,63.23,64,64,0.958,0.03447 -12,VBS46311-6321STDY9453311,61.87,63,63,62.59,63,64,61.86,63,63,64.63,65,65,57.85,59,61,61.49,62,62,0.958,0.03439 -13,VBS46312-6321STDY9453312,73.44,75,76,73.98,75,76,73.41,75,76,75.79,76,76,69.98,72,74,73.31,75,75,0.959,0.0345 -14,VBS46313-6321STDY9453313,53.08,54,54,53.62,54,54,53.13,54,54,55.22,55,55,49.87,51,53,52.85,54,53,0.959,0.03427 -15,VBS46314-6321STDY9453314,46.94,48,48,47.42,48,48,46.97,47,48,48.91,49,49,43.98,45,46,46.76,47,48,0.959,0.03424 -16,VBS46315-6321STDY9453315,40.19,40,40,40.49,41,41,40.18,40,40,41.62,41,41,38.19,39,39,40.06,40,40,0.956,0.03426 -17,VBS46316-6321STDY9453316,50.42,51,51,50.86,51,52,50.34,51,51,52.46,53,53,47.63,49,50,50.25,51,51,0.957,0.03433 -18,VBS46317-6321STDY9453317,56.41,57,58,56.99,58,58,56.45,57,57,58.84,59,59,52.81,54,56,56.17,57,57,0.959,0.0343 -19,VBS46318-6321STDY9453318,60.31,61,62,60.96,62,62,60.39,61,61,62.89,63,63,56.35,58,59,60.12,61,62,0.961,0.03434 -20,VBS46319-6321STDY9453319,55.85,57,57,56.41,57,57,55.8,56,57,58.31,58,58,52.45,54,55,55.54,56,56,0.957,0.03435 -21,VBS46320-6321STDY9453320,53.39,54,55,53.77,54,55,53.38,54,55,55.44,56,55,50.6,52,53,53.18,54,55,0.957,0.03434 -22,VBS46321-6321STDY9453321,69.25,70,71,70.16,71,72,69.19,70,71,72.5,73,73,64.38,67,69,68.95,70,71,0.96,0.03429 -23,VBS46322-6321STDY9453322,76.33,78,78,77.0,78,79,76.25,78,78,79.39,80,80,72.09,75,76,76.0,78,78,0.958,0.03438 -24,VBS46323-6321STDY9453323,50.47,51,52,50.99,52,52,50.51,51,51,52.64,53,53,47.38,49,50,50.14,51,51,0.959,0.03426 -25,VBS46324-6321STDY9453324,47.33,48,48,47.78,48,49,47.28,48,48,49.09,49,49,44.91,46,47,47.01,48,48,0.957,0.0343 -26,VBS46325-6321STDY9453325,64.46,65,66,65.24,66,66,64.38,65,66,67.53,68,68,60.2,62,63,63.97,65,65,0.958,0.03439 -27,VBS46326-6321STDY9453326,57.67,58,59,58.34,59,59,57.73,58,58,60.27,60,60,53.65,55,57,57.48,58,59,0.96,0.03432 -28,VBS46327-6321STDY9453327,63.05,64,64,63.63,64,65,62.97,64,64,65.63,66,66,59.43,61,63,62.83,64,64,0.958,0.0344 -29,VBS46328-6321STDY9453328,56.21,57,57,56.79,57,58,56.29,57,58,58.57,59,59,52.63,54,55,55.95,57,57,0.959,0.03423 -30,VBS46329-6321STDY9453329,62.43,63,64,62.99,64,64,62.48,63,64,64.93,65,65,58.89,61,62,62.05,63,63,0.958,0.03439 -31,VBS46330-6321STDY9453330,67.2,68,69,67.98,69,69,67.11,68,68,70.18,70,70,62.79,64,66,66.97,68,69,0.958,0.03445 -32,VBS46331-6321STDY9453331,53.05,54,54,53.73,54,54,53.12,54,54,55.63,56,55,49.1,50,51,52.74,53,54,0.959,0.03424 -33,VBS46332-6321STDY9453332,32.34,32,32,32.43,32,32,32.3,32,32,33.45,33,33,30.72,31,32,32.62,33,33,0.958,0.03412 -34,VBS46333-6321STDY9453333,59.06,59,59,59.92,60,59,58.94,59,59,61.85,62,61,54.62,55,56,58.97,59,59,0.957,0.03442 -35,VBS46334-6321STDY9453334,59.96,61,61,60.67,61,61,59.99,61,61,62.7,63,63,55.97,57,58,59.49,60,61,0.958,0.0343 -36,VBS46335-6321STDY9453335,66.27,67,68,67.01,68,69,66.31,67,68,69.36,70,70,61.73,64,66,65.94,67,68,0.961,0.03436 -37,VBS46336-6321STDY9453336,54.48,55,55,55.03,56,56,54.46,55,55,56.94,57,57,51.12,52,53,54.09,55,55,0.958,0.03428 -38,VBS46337-6321STDY9453337,46.2,47,47,46.67,47,47,46.16,46,47,47.99,48,47,43.58,44,46,45.98,46,47,0.957,0.03426 -39,VBS46338-6321STDY9453338,49.41,50,50,49.9,50,51,49.54,50,50,51.4,51,51,46.42,48,48,49.09,50,50,0.959,0.03421 -40,VBS46339-6321STDY9453339,58.79,59,59,59.58,60,60,58.66,59,59,61.93,62,61,54.38,55,57,58.41,59,59,0.957,0.03436 -41,VBS46340-6321STDY9453340,55.71,56,57,56.39,57,57,55.77,56,56,58.7,59,58,51.33,53,53,55.44,56,56,0.959,0.0343 -42,VBS46341-6321STDY9453341,50.85,51,51,51.53,52,52,50.85,51,51,53.54,53,53,46.94,48,49,50.45,51,51,0.957,0.03431 -43,VBS46342-6321STDY9453342,64.95,66,66,65.69,66,66,64.93,66,66,68.1,68,68,60.45,62,63,64.55,66,66,0.96,0.03433 -44,VBS46343-6321STDY9453343,53.7,54,54,54.3,55,55,53.54,54,53,56.01,56,55,49.93,51,52,54.05,55,54,0.958,0.03425 -45,VBS46344-6321STDY9453344,40.85,41,41,41.28,41,41,40.87,41,41,42.55,42,42,38.45,39,40,40.49,41,41,0.956,0.03424 -46,VBS46345-6321STDY9453345,68.49,70,70,69.4,70,71,68.49,69,70,71.95,72,72,63.35,65,66,68.14,69,70,0.96,0.03438 +sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,frac_gen_cov,divergence,contam_pct,contam_LLR +VBS46299-6321STDY9453299,41.48,42,42,42.02,42,43,41.69,42,42,43.08,43,43,0.946,0.03433,, +VBS46300-6321STDY9453300,52.17,53,53,53.0,54,54,52.56,53,54,54.34,55,55,0.946,0.03436,, +VBS46301-6321STDY9453301,67.16,68,69,68.26,69,70,67.76,69,69,70.22,71,71,0.948,0.03442,, +VBS46302-6321STDY9453302,61.92,63,63,63.09,64,64,62.5,63,64,64.97,65,65,0.947,0.03441,, +VBS46303-6321STDY9453303,44.15,44,45,44.67,45,45,44.25,45,45,45.88,46,46,0.947,0.03424,, +VBS46304-6321STDY9453304,62.75,63,64,63.72,64,65,63.19,64,65,65.51,66,66,0.948,0.03448,, +VBS46305-6321STDY9453305,65.69,67,67,67.22,68,68,66.65,68,67,69.32,70,69,0.947,0.03441,, +VBS46306-6321STDY9453306,54.83,55,56,55.87,56,57,55.26,56,57,57.67,58,58,0.946,0.03434,, +VBS46307-6321STDY9453307,47.43,48,48,48.35,49,49,47.96,48,49,49.81,50,49,0.947,0.03415,, +VBS46308-6321STDY9453308,60.25,61,62,61.42,62,63,60.85,62,62,63.53,64,63,0.947,0.03438,, +VBS46309-6321STDY9453309,56.48,57,58,57.43,58,58,56.96,58,58,58.55,59,59,0.949,0.03429,, +VBS46310-6321STDY9453310,63.6,64,64,63.85,64,64,63.43,64,65,64.99,65,65,0.948,0.03447,, +VBS46311-6321STDY9453311,61.12,62,62,62.59,63,64,61.86,63,63,64.63,65,65,0.947,0.03439,, +VBS46312-6321STDY9453312,73.02,74,75,73.98,75,76,73.41,75,76,75.79,76,76,0.949,0.0345,, +VBS46313-6321STDY9453313,52.73,53,54,53.62,54,54,53.13,54,54,55.22,55,55,0.947,0.03427,, +VBS46314-6321STDY9453314,46.57,47,47,47.42,48,48,46.97,47,48,48.91,49,49,0.947,0.03424,, +VBS46315-6321STDY9453315,40.01,40,40,40.49,41,41,40.18,40,40,41.62,41,41,0.946,0.03426,, +VBS46316-6321STDY9453316,49.96,50,51,50.86,51,52,50.34,51,51,52.46,53,53,0.946,0.03433,, +VBS46317-6321STDY9453317,55.85,56,57,56.99,58,58,56.45,57,57,58.84,59,59,0.947,0.0343,, +VBS46318-6321STDY9453318,59.71,60,61,60.96,62,62,60.39,61,61,62.89,63,63,0.95,0.03434,, +VBS46319-6321STDY9453319,55.26,56,56,56.41,57,57,55.8,56,57,58.31,58,58,0.947,0.03435,, +VBS46320-6321STDY9453320,53.04,54,54,53.77,54,55,53.38,54,55,55.44,56,55,0.947,0.03434,, +VBS46321-6321STDY9453321,68.33,69,70,70.16,71,72,69.19,70,71,72.5,73,73,0.949,0.03429,, +VBS46322-6321STDY9453322,75.5,77,78,77.0,78,79,76.25,78,78,79.39,80,80,0.948,0.03438,, +VBS46323-6321STDY9453323,50.12,51,51,50.99,52,52,50.51,51,51,52.64,53,53,0.947,0.03426,, +VBS46324-6321STDY9453324,46.98,47,48,47.78,48,49,47.28,48,48,49.09,49,49,0.946,0.0343,, +VBS46325-6321STDY9453325,63.62,64,65,65.24,66,66,64.38,65,66,67.53,68,68,0.947,0.03439,, +VBS46326-6321STDY9453326,57.02,57,58,58.34,59,59,57.73,58,58,60.27,60,60,0.948,0.03432,, +VBS46327-6321STDY9453327,62.41,63,64,63.63,64,65,62.97,64,64,65.63,66,66,0.948,0.0344,, +VBS46328-6321STDY9453328,55.71,56,57,56.79,57,58,56.29,57,58,58.57,59,59,0.948,0.03423,, +VBS46329-6321STDY9453329,61.8,63,63,62.99,64,64,62.48,63,64,64.93,65,65,0.947,0.03439,, +VBS46330-6321STDY9453330,66.21,67,67,67.98,69,69,67.11,68,68,70.18,70,70,0.947,0.03445,, +VBS46331-6321STDY9453331,52.38,53,53,53.73,54,54,53.12,54,54,55.63,56,55,0.948,0.03424,, +VBS46332-6321STDY9453332,32.16,32,32,32.43,32,32,32.3,32,32,33.45,33,33,0.946,0.03412,, +VBS46333-6321STDY9453333,58.05,58,58,59.92,60,59,58.94,59,59,61.85,62,61,0.947,0.03442,, +VBS46334-6321STDY9453334,59.16,60,60,60.67,61,61,59.99,61,61,62.7,63,63,0.948,0.0343,, +VBS46335-6321STDY9453335,65.54,67,67,67.01,68,69,66.31,67,68,69.36,70,70,0.95,0.03436,, +VBS46336-6321STDY9453336,53.9,54,55,55.03,56,56,54.46,55,55,56.94,57,57,0.948,0.03428,, 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b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv index fa5b7c3ea..a8191fed0 100644 --- a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv @@ -1,27 +1,27 @@ -,sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence -0,VBS45687-6143STDY8787412,32.18,32,32,32.03,32,32,32.37,32,32,32.26,32,32,32.16,32,32,32.07,32,31,0.983,0.01374 -1,VBS45688-6143STDY8787413,33.19,33,33,33.0,33,33,33.35,33,33,33.27,33,33,33.24,33,33,33.14,33,33,0.984,0.01378 -2,VBS45689-6143STDY8787414,34.26,34,34,34.05,34,34,34.53,34,34,34.29,34,34,34.26,34,34,34.19,34,33,0.984,0.01378 -3,VBS45690-6143STDY8787415,33.07,33,33,32.91,33,33,33.32,33,33,33.19,33,33,33.0,33,33,32.89,33,33,0.984,0.01377 -4,VBS45691-6143STDY8787416,34.81,35,34,34.77,35,34,35.02,35,34,35.07,35,35,34.36,34,35,34.7,35,35,0.984,0.01377 -5,VBS45692-6143STDY8787417,31.07,31,31,30.85,31,31,31.24,31,31,31.11,31,31,31.13,31,31,31.14,31,31,0.983,0.01377 -8,VBS45701-6143STDY8787420,9.96,9,9,9.91,9,9,10.07,9,9,9.94,9,9,9.91,9,9,9.96,9,9,0.981,0.01546 -9,VBS45702-6143STDY8787421,8.77,8,8,8.76,8,8,8.81,8,8,8.85,8,8,8.67,8,8,8.74,8,8,0.981,0.01543 -12,VBS45708-6143STDY8787424,10.22,10,9,10.23,10,9,10.32,10,9,10.38,10,9,9.9,9,9,10.19,10,9,0.981,0.01538 -13,VBS45709-6143STDY8787425,8.32,8,7,8.31,8,7,8.43,8,7,8.4,8,7,8.1,7,7,8.29,8,7,0.98,0.01539 -14,VBS45711-6143STDY8787426,9.93,9,9,9.94,9,9,10.05,9,9,10.06,9,9,9.62,9,9,9.88,9,9,0.982,0.01536 -15,VBS45713-6143STDY8787427,23.63,23,23,23.54,23,23,23.78,23,23,23.77,23,23,23.41,23,23,23.64,23,23,0.983,0.01382 -17,VBS45717-6143STDY8787429,34.14,34,34,33.83,34,34,34.26,34,34,34.18,34,34,34.39,34,34,34.19,34,34,0.984,0.01375 -18,VBS45718-6143STDY8787430,35.17,35,35,34.87,35,35,35.34,35,35,35.21,35,35,35.29,35,35,35.26,35,35,0.984,0.01387 -19,VBS45720-6143STDY8787431,38.61,38,38,38.39,38,38,38.81,39,38,38.61,39,38,38.61,39,38,38.71,39,39,0.984,0.0138 -20,VBS45723-6143STDY8787432,39.79,40,40,39.73,40,40,40.05,40,40,40.21,40,40,39.09,39,39,39.73,40,40,0.984,0.01373 -21,VBS45724-6143STDY8787433,34.51,34,34,34.28,34,34,34.63,34,34,34.74,35,34,34.46,34,34,34.51,34,34,0.984,0.01378 -22,VBS45728-6143STDY8787434,49.49,49,49,49.16,49,49,49.6,49,49,49.69,50,50,49.47,50,50,49.73,50,49,0.984,0.0138 -23,VBS45734-6143STDY8787435,33.45,33,33,33.27,33,33,33.67,33,33,33.43,33,33,33.65,33,33,33.23,33,33,0.984,0.01379 -24,VBS45735-6143STDY8787436,33.51,33,33,33.25,33,33,33.58,33,33,33.75,34,33,33.47,33,33,33.7,34,33,0.984,0.01378 -25,VBS45737-6143STDY8787437,38.95,39,39,38.77,39,38,39.12,39,39,39.23,39,39,38.87,39,39,38.77,39,38,0.984,0.01379 -26,VBS45738-6143STDY8787438,39.63,40,39,39.44,39,39,39.84,40,39,39.87,40,39,39.46,39,39,39.57,39,39,0.984,0.01378 -27,VBS45739-6143STDY8787439,38.75,39,38,38.43,38,38,39.04,39,39,38.71,39,38,39.04,39,39,38.59,38,38,0.984,0.01376 -28,VBS45742-6143STDY8787440,43.47,43,43,43.37,43,44,43.52,43,43,43.55,43,43,43.32,43,43,43.61,43,43,0.984,0.01376 -29,VBS45743-6143STDY8787441,41.01,41,41,41.0,41,41,41.3,41,41,41.51,41,41,40.23,40,40,40.81,41,41,0.984,0.01376 -30,VBS45745-6143STDY8787442,46.48,46,46,46.58,46,46,46.9,46,46,47.01,47,46,45.45,45,45,46.04,46,46,0.984,0.01381 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a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1277-VO-KH-WITKOWSKI-VMF00183/sequence_qc_stats.csv @@ -1,249 +1,249 @@ -,sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence -0,VBS54551-6143STDY11462443,24.37,24,24,24.35,24,24,24.47,24,24,24.41,24,24,24.11,24,23,24.46,24,24,0.982,0.01406 -1,VBS54553-6143STDY11462445,25.31,25,25,25.39,25,25,25.53,25,25,25.8,26,25,24.26,24,23,25.34,25,24,0.983,0.01392 -2,VBS54554-6143STDY11462446,21.73,21,20,21.62,21,20,21.78,21,20,21.45,21,20,22.02,21,21,21.87,21,20,0.982,0.0143 -3,VBS54555-6143STDY11462447,12.71,11,8,12.7,11,8,12.82,11,8,11.48,10,8,13.55,12,9,13.04,11,9,0.976,0.01665 -4,VBS54556-6143STDY11462448,24.43,24,24,24.37,24,24,24.54,24,23,24.4,24,24,24.36,24,24,24.47,24,23,0.982,0.01416 -5,VBS54557-6143STDY11462449,27.11,26,24,26.88,26,24,27.22,26,24,26.17,25,24,27.93,27,25,27.56,27,25,0.982,0.01417 -6,VBS54558-6143STDY11462450,10.37,10,8,10.54,10,9,10.42,10,8,11.26,11,9,9.02,8,7,10.31,10,8,0.978,0.01598 -8,VBS54561-6143STDY11462453,29.15,29,28,29.26,29,28,29.32,29,29,29.6,29,29,28.15,28,28,29.23,29,28,0.983,0.01387 -9,VBS54562-6143STDY11462454,26.39,26,25,26.75,26,26,26.52,26,25,28.0,28,27,23.95,23,23,26.21,26,25,0.983,0.01393 -10,VBS54563-6143STDY11462455,31.37,31,31,31.27,31,31,31.61,31,31,31.57,31,31,31.01,31,30,31.3,31,31,0.983,0.01379 -11,VBS54564-6143STDY11462456,32.5,32,32,32.43,32,32,32.77,32,32,32.75,33,32,31.98,32,31,32.42,32,32,0.983,0.01377 -12,VBS54565-6143STDY11462457,35.72,35,35,35.75,36,35,35.98,36,35,36.46,36,36,34.55,34,34,35.63,35,36,0.984,0.01377 -13,VBS54567-6143STDY11462459,35.59,35,35,35.55,35,35,35.77,35,35,36.19,36,35,34.77,34,34,35.57,35,35,0.983,0.01379 -14,VBS54569-6143STDY11462461,12.99,13,12,13.13,13,12,13.06,12,12,13.55,13,13,12.04,11,11,12.98,13,12,0.981,0.01793 -15,VBS54570-6143STDY11462462,23.94,24,23,24.15,24,23,24.12,24,23,25.02,25,24,22.25,22,21,23.78,23,23,0.983,0.01394 -16,VBS54571-6143STDY11462463,15.9,15,15,15.8,15,15,16.0,15,15,15.52,15,14,16.15,15,15,16.05,15,15,0.981,0.01532 -17,VBS54572-6143STDY11462464,29.98,30,29,29.96,30,30,30.23,30,30,30.42,30,30,29.19,29,29,29.93,30,29,0.983,0.01378 -19,VBS54574-6143STDY11462466,23.01,23,22,23.32,23,23,23.1,23,22,24.53,24,23,20.85,20,20,22.79,22,22,0.982,0.01402 -20,VBS54575-6143STDY11462467,19.28,19,18,19.72,19,18,19.39,19,18,20.96,20,19,16.67,16,15,19.08,18,17,0.982,0.01468 -21,VBS54576-6143STDY11462468,27.1,27,26,27.35,27,27,27.25,27,26,28.56,28,28,24.87,24,24,27.06,27,26,0.983,0.01383 -22,VBS54577-6143STDY11462469,25.78,25,25,25.85,25,25,25.99,25,25,26.54,26,26,24.6,24,24,25.69,25,25,0.983,0.01393 -23,VBS54578-6143STDY11462470,31.36,31,31,31.31,31,31,31.61,31,31,31.48,31,31,31.01,31,30,31.28,31,31,0.983,0.01381 -24,VBS54579-6143STDY11462471,21.31,21,20,21.69,21,21,21.41,21,20,22.84,22,21,18.98,18,17,21.14,21,20,0.982,0.01433 -25,VBS54580-6143STDY11462472,33.76,33,33,33.64,33,33,34.01,33,32,33.28,33,33,33.97,33,33,33.92,33,33,0.983,0.01384 -26,VBS54581-6143STDY11462473,18.0,17,17,17.96,17,17,18.09,17,17,18.32,18,17,17.6,17,16,17.95,17,17,0.981,0.01738 -27,VBS54582-6143STDY11462474,11.96,11,10,12.2,12,11,12.07,11,10,12.85,12,11,10.47,10,9,11.84,11,10,0.981,0.01615 -28,VBS54583-6143STDY11462475,18.06,17,17,18.33,18,17,18.19,18,17,19.37,19,18,16.06,15,15,17.95,17,17,0.982,0.01476 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b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/curation/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv @@ -1,220 +1,220 @@ -,sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence -0,VBS45974-6296STDY9478582,9.79,9,9,9.79,9,9,9.81,9,9,9.91,10,9,9.81,9,9,9.62,9,9,0.952,0.03652 -1,VBS45975-6296STDY10244530,75.33,76,75,74.27,74,75,74.89,75,75,76.6,76,75,76.95,78,77,74.97,75,75,0.959,0.03382 -2,VBS45976-6296STDY9478584,12.9,13,12,12.95,13,12,12.87,13,12,13.16,13,12,12.6,12,12,12.83,13,12,0.952,0.03517 -3,VBS45979-6296STDY9478587,14.53,14,14,14.56,14,14,14.39,14,14,14.72,14,14,14.56,14,14,14.42,14,14,0.954,0.03525 -5,VBS45982-6296STDY9478589,20.34,19,18,20.91,20,19,20.46,19,18,20.86,20,18,19.02,18,17,19.81,19,18,0.955,0.03414 -6,VBS45983-6296STDY10244537,16.39,16,16,16.38,16,16,16.34,16,16,16.93,17,16,16.07,16,16,16.19,16,16,0.955,0.03482 -7,VBS45984-6296STDY10244538,36.46,37,37,36.39,36,36,36.38,36,37,37.05,37,37,36.14,36,37,36.36,36,37,0.957,0.03366 -8,VBS45985-6296STDY10244539,37.61,38,38,37.81,38,38,37.37,37,38,38.91,39,38,36.55,37,36,37.22,37,37,0.957,0.03361 -9,VBS45986-6296STDY10244540,42.12,42,42,42.54,43,42,42.04,42,42,43.8,44,43,40.26,41,41,41.4,42,41,0.956,0.03393 -10,VBS45987-6296STDY10244541,37.26,37,37,37.56,37,37,37.37,37,37,38.76,39,38,35.6,36,36,36.47,37,36,0.957,0.03383 -11,VBS45988-6296STDY10244542,38.39,39,39,38.55,39,39,38.36,38,39,39.36,39,39,37.31,38,38,38.11,38,39,0.958,0.03386 -12,VBS45989-6296STDY10244543,49.81,50,50,49.82,50,50,49.57,50,50,51.36,51,51,48.79,49,49,49.44,50,50,0.957,0.03365 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Laurent,Cambodia,Preah Kleang,2014,3,13.667,104.982 +VBS09547-4248STDY7309009,VBS09547-4248STDY7309009,KV-22-00495,Brandy St. Laurent,Cambodia,Preah Kleang,2014,3,13.667,104.982 +VBS09549-4248STDY7309010,VBS09549-4248STDY7309010,KV-22-00700,Brandy St. Laurent,Cambodia,Preah Kleang,2014,3,13.667,104.982 +VBS09551-4248STDY7309011,VBS09551-4248STDY7309011,KV-22-00050,Brandy St. Laurent,Cambodia,Preah Kleang,2014,3,13.667,104.982 +VBS09552-4248STDY7309012,VBS09552-4248STDY7309012,KV-22-00486,Brandy St. Laurent,Cambodia,Preah Kleang,2014,3,13.667,104.982 +VBS09553-4248STDY7309013,VBS09553-4248STDY7309013,KV-22-00686,Brandy St. Laurent,Cambodia,Preah Kleang,2014,3,13.667,104.982 +VBS09555-4248STDY7309015,VBS09555-4248STDY7309015,KV-21-01436,Brandy St. Laurent,Cambodia,Chean Mok,2014,4,13.770,104.920 +VBS09558-4248STDY7309017,VBS09558-4248STDY7309017,KV-21-00871,Brandy St. Laurent,Cambodia,Chean Mok,2014,4,13.770,104.920 +VBS09570-4248STDY7309020,VBS09570-4248STDY7309020,KV-22-00231,Brandy St. Laurent,Cambodia,Preah Kleang,2014,4,13.667,104.982 +VBS09571-4248STDY7309021,VBS09571-4248STDY7309021,KV-22-00179,Brandy St. Laurent,Cambodia,Preah Kleang,2014,4,13.667,104.982 +VBS09572-4248STDY7309022,VBS09572-4248STDY7309022,KV-22-00340,Brandy St. Laurent,Cambodia,Preah Kleang,2014,4,13.667,104.982 +VBS09575-4248STDY7309023,VBS09575-4248STDY7309023,KV-21-01419,Brandy St. Laurent,Cambodia,Chean Mok,2014,6,13.770,104.920 +VBS09579-4248STDY7309025,VBS09579-4248STDY7309025,KV-21-01288,Brandy St. Laurent,Cambodia,Chean Mok,2014,6,13.770,104.920 +VBS09580-4248STDY7309026,VBS09580-4248STDY7309026,KV-21-01472,Brandy St. Laurent,Cambodia,Chean Mok,2014,6,13.770,104.920 +VBS09581-4248STDY7309027,VBS09581-4248STDY7309027,KV-21-01456,Brandy St. Laurent,Cambodia,Chean Mok,2014,6,13.770,104.920 +VBS09582-4248STDY7309028,VBS09582-4248STDY7309028,KV-21-01748,Brandy St. Laurent,Cambodia,Chean Mok,2014,6,13.770,104.920 +VBS09583-4248STDY7309029,VBS09583-4248STDY7309029,KV-21-01460,Brandy St. Laurent,Cambodia,Chean Mok,2014,6,13.770,104.920 +VBS09590-4248STDY7309030,VBS09590-4248STDY7309030,KV-21-01705,Brandy St. Laurent,Cambodia,Chean Mok,2014,6,13.770,104.920 +VBS09593-4248STDY7309031,VBS09593-4248STDY7309031,KV-21-00992,Brandy St. Laurent,Cambodia,Chean Mok,2014,6,13.770,104.920 +VBS09639-4248STDY7309033,VBS09639-4248STDY7309033,KV-21-02733,Brandy St. Laurent,Cambodia,Chean Mok,2014,9,13.770,104.920 +VBS09644-4248STDY7309035,VBS09644-4248STDY7309035,KV-21-02520,Brandy St. Laurent,Cambodia,Chean Mok,2014,9,13.770,104.920 +VBS09648-4248STDY7309037,VBS09648-4248STDY7309037,KV-21-02599,Brandy St. Laurent,Cambodia,Chean Mok,2014,9,13.770,104.920 +VBS09649-4248STDY7309038,VBS09649-4248STDY7309038,KV-21-02632,Brandy St. Laurent,Cambodia,Chean Mok,2014,9,13.770,104.920 +VBS09650-4248STDY7309039,VBS09650-4248STDY7309039,KV-21-02658,Brandy St. Laurent,Cambodia,Chean Mok,2014,9,13.770,104.920 +VBS09651-4248STDY7309040,VBS09651-4248STDY7309040,KV-22-01945,Brandy St. Laurent,Cambodia,Preah Kleang,2014,9,13.667,104.982 +VBS09652-4248STDY7309041,VBS09652-4248STDY7309041,KV-22-00838,Brandy St. Laurent,Cambodia,Preah Kleang,2014,9,13.667,104.982 +VBS09654-4248STDY7309042,VBS09654-4248STDY7309042,KV-22-01031,Brandy St. Laurent,Cambodia,Preah Kleang,2014,9,13.667,104.982 +VBS09655-4248STDY7309043,VBS09655-4248STDY7309043,KV-22-00846,Brandy St. Laurent,Cambodia,Preah Kleang,2014,9,13.667,104.982 +VBS09656-4248STDY7309044,VBS09656-4248STDY7309044,KV-22-01046,Brandy St. Laurent,Cambodia,Preah Kleang,2014,9,13.667,104.982 +VBS09657-4248STDY7309045,VBS09657-4248STDY7309045,KV-22-01950,Brandy St. Laurent,Cambodia,Preah Kleang,2014,9,13.667,104.982 +VBS09660-4248STDY7309047,VBS09660-4248STDY7309047,KV-21-02473,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09661-4248STDY7309048,VBS09661-4248STDY7309048,KV-21-02381,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09662-4248STDY7309049,VBS09662-4248STDY7309049,KV-21-03163,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09663-4248STDY7309050,VBS09663-4248STDY7309050,KV-21-02412,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09672-4248STDY7309051,VBS09672-4248STDY7309051,KV-21-02464,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09673-4248STDY7309052,VBS09673-4248STDY7309052,KV-21-02430,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09674-4248STDY7309053,VBS09674-4248STDY7309053,KV-22-01576,Brandy St. Laurent,Cambodia,Preah Kleang,2014,10,13.667,104.982 +VBS09675-4248STDY7309054,VBS09675-4248STDY7309054,KV-22-01646,Brandy St. Laurent,Cambodia,Preah Kleang,2014,10,13.667,104.982 +VBS09677-4248STDY7309056,VBS09677-4248STDY7309056,KV-22-01583,Brandy St. Laurent,Cambodia,Preah Kleang,2014,10,13.667,104.982 +VBS09681-4248STDY7309058,VBS09681-4248STDY7309058,KV-22-00811,Brandy St. Laurent,Cambodia,Preah Kleang,2014,10,13.667,104.982 +VBS09685-4248STDY7309059,VBS09685-4248STDY7309059,KV-22-01001,Brandy St. Laurent,Cambodia,Preah Kleang,2014,10,13.667,104.982 +VBS09686-4248STDY7309060,VBS09686-4248STDY7309060,KV-22-00981,Brandy St. Laurent,Cambodia,Preah Kleang,2014,10,13.667,104.982 +VBS09689-4248STDY7309061,VBS09689-4248STDY7309061,KV-22-00314,Brandy St. Laurent,Cambodia,Preah Kleang,2014,10,13.667,104.982 +VBS09695-4248STDY7309062,VBS09695-4248STDY7309062,KV-21-03694,Brandy St. Laurent,Cambodia,Chean Mok,2014,12,13.770,104.920 +VBS09699-4248STDY7309063,VBS09699-4248STDY7309063,KV-21-03771,Brandy St. Laurent,Cambodia,Chean Mok,2014,12,13.770,104.920 +VBS09712-4248STDY7309064,VBS09712-4248STDY7309064,KV-21-03629,Brandy St. Laurent,Cambodia,Chean Mok,2014,12,13.770,104.920 +VBS09713-4248STDY7309065,VBS09713-4248STDY7309065,KV-21-03397,Brandy St. Laurent,Cambodia,Chean Mok,2014,12,13.770,104.920 +VBS09730-4248STDY7309066,VBS09730-4248STDY7309066,KV-21-03898,Brandy St. Laurent,Cambodia,Chean Mok,2015,1,13.770,104.920 +VBS09734-4248STDY7309067,VBS09734-4248STDY7309067,KV-21-02983,Brandy St. Laurent,Cambodia,Chean Mok,2015,1,13.770,104.920 +VBS09738-4248STDY7309069,VBS09738-4248STDY7309069,KV-21-02218,Brandy St. Laurent,Cambodia,Chean Mok,2015,1,13.770,104.920 +VBS09744-4248STDY7309072,VBS09744-4248STDY7309072,KV-21-02985,Brandy St. Laurent,Cambodia,Chean Mok,2015,1,13.770,104.920 +VBS09747-4248STDY7309076,VBS09747-4248STDY7309076,KV-22-00907,Brandy St. Laurent,Cambodia,Preah Kleang,2015,1,13.667,104.982 +VBS09765-4248STDY7309077,VBS09765-4248STDY7309077,KV-31-03653,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09778-4248STDY7309079,VBS09778-4248STDY7309079,KV-32-04546,Brandy St. Laurent,Cambodia,Sayas,2015,1,13.548,107.025 +VBS09790-4248STDY7309081,VBS09790-4248STDY7309081,KV-31-00552,Brandy St. Laurent,Cambodia,Chamkar San,2014,3,13.595,106.995 +VBS09802-4248STDY7309083,VBS09802-4248STDY7309083,KV-32-01581,Brandy St. Laurent,Cambodia,Sayas,2014,3,13.548,107.025 +VBS09815-4248STDY7309084,VBS09815-4248STDY7309084,KV-31-00581,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09817-4248STDY7309085,VBS09817-4248STDY7309085,KV-31-00599,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09829-4248STDY7309086,VBS09829-4248STDY7309086,KV-31-00631,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09832-4248STDY7309087,VBS09832-4248STDY7309087,KV-32-01436,Brandy St. Laurent,Cambodia,Sayas,2014,4,13.548,107.025 +VBS09833-4248STDY7309088,VBS09833-4248STDY7309088,KV-32-01430,Brandy St. Laurent,Cambodia,Sayas,2014,4,13.548,107.025 +VBS09836-4248STDY7309089,VBS09836-4248STDY7309089,KV-32-01611,Brandy St. Laurent,Cambodia,Sayas,2014,4,13.548,107.025 +VBS09839-4248STDY7309090,VBS09839-4248STDY7309090,KV-32-01464,Brandy St. Laurent,Cambodia,Sayas,2014,4,13.548,107.025 +VBS09843-4248STDY7309091,VBS09843-4248STDY7309091,KV-32-01387,Brandy St. Laurent,Cambodia,Sayas,2014,4,13.548,107.025 +VBS09851-4248STDY7309092,VBS09851-4248STDY7309092,KV-31-01313,Brandy St. Laurent,Cambodia,Chamkar San,2014,6,13.595,106.995 +VBS09852-4248STDY7309093,VBS09852-4248STDY7309093,KV-31-01315,Brandy St. Laurent,Cambodia,Chamkar San,2014,6,13.595,106.995 +VBS09858-4248STDY7309094,VBS09858-4248STDY7309094,KV-31-01336,Brandy St. Laurent,Cambodia,Chamkar San,2014,6,13.595,106.995 +VBS09861-4248STDY7309095,VBS09861-4248STDY7309095,KV-31-01277,Brandy St. Laurent,Cambodia,Chamkar San,2014,6,13.595,106.995 +VBS09871-4248STDY7309097,VBS09871-4248STDY7309097,KV-31-01412,Brandy St. Laurent,Cambodia,Chamkar San,2014,6,13.595,106.995 +VBS09917-4248STDY7309098,VBS09917-4248STDY7309098,KV-31-02129,Brandy St. Laurent,Cambodia,Chamkar San,2014,9,13.595,106.995 +VBS09921-4248STDY7309100,VBS09921-4248STDY7309100,KV-32-04634,Brandy St. Laurent,Cambodia,Sayas,2014,9,13.548,107.025 +VBS09957-4248STDY7309104,VBS09957-4248STDY7309104,KV-32-03883,Brandy St. Laurent,Cambodia,Sayas,2014,12,13.548,107.025 +VBS09963-4248STDY7309105,VBS09963-4248STDY7309105,KV-32-04246,Brandy St. Laurent,Cambodia,Sayas,2014,12,13.548,107.025 +VBS09966-4248STDY7309106,VBS09966-4248STDY7309106,KV-32-04479,Brandy St. Laurent,Cambodia,Sayas,2014,12,13.548,107.025 +VBS09967-4248STDY7309107,VBS09967-4248STDY7309107,KV-32-04323,Brandy St. Laurent,Cambodia,Sayas,2014,12,13.548,107.025 +VBS09971-4248STDY7309108,VBS09971-4248STDY7309108,KV-32-04207,Brandy St. Laurent,Cambodia,Sayas,2014,12,13.548,107.025 +VBS09979-4248STDY7309109,VBS09979-4248STDY7309109,KV-31-03418,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS10021-4248STDY7309112,VBS10021-4248STDY7309112,15908,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS10022-4248STDY7309113,VBS10022-4248STDY7309113,14716,Brandy St. Laurent,Cambodia,Thmar Da,2010,12,12.155,102.735 +VBS10025-4248STDY7309114,VBS10025-4248STDY7309114,15914,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS10026-4248STDY7309115,VBS10026-4248STDY7309115,15038,Brandy St. Laurent,Cambodia,Thmar Da,2010,12,12.155,102.735 +VBS10027-4248STDY7309116,VBS10027-4248STDY7309116,15021,Brandy St. Laurent,Cambodia,Thmar Da,2010,12,12.155,102.735 +VBS10028-4248STDY7309117,VBS10028-4248STDY7309117,14608,Brandy St. Laurent,Cambodia,Thmar Da,2010,12,12.155,102.735 +VBS10029-4248STDY7309118,VBS10029-4248STDY7309118,14770,Brandy St. Laurent,Cambodia,Thmar Da,2010,12,12.155,102.735 +VBS10032-4248STDY7309119,VBS10032-4248STDY7309119,14964,Brandy St. Laurent,Cambodia,Thmar Da,2011,4,12.155,102.735 +VBS10033-4248STDY7309120,VBS10033-4248STDY7309120,15142,Brandy St. Laurent,Cambodia,Thmar Da,2010,12,12.155,102.735 +VBS10034-4248STDY7309121,VBS10034-4248STDY7309121,15848,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS10035-4248STDY7309122,VBS10035-4248STDY7309122,14600,Brandy St. Laurent,Cambodia,Thmar Da,2010,12,12.155,102.735 +VBS10036-4248STDY7309123,VBS10036-4248STDY7309123,15300,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS10038-4248STDY7309124,VBS10038-4248STDY7309124,14930,Brandy St. Laurent,Cambodia,Thmar Da,2011,4,12.155,102.735 +VBS10039-4248STDY7309125,VBS10039-4248STDY7309125,14748,Brandy St. Laurent,Cambodia,Thmar Da,2010,12,12.155,102.735 +VBS10040-4248STDY7309126,VBS10040-4248STDY7309126,15928,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS10042-4248STDY7309127,VBS10042-4248STDY7309127,15930,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS10043-4248STDY7309128,VBS10043-4248STDY7309128,15810,Brandy St. Laurent,Cambodia,Thmar Da,2011,2,12.155,102.735 +VBS10044-4248STDY7309129,VBS10044-4248STDY7309129,9309,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS10049-4248STDY7309130,VBS10049-4248STDY7309130,14842,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS10052-4248STDY7309131,VBS10052-4248STDY7309131,15167,Brandy St. Laurent,Cambodia,Thmar Da,2011,2,12.155,102.735 +VBS10055-4248STDY7309132,VBS10055-4248STDY7309132,14892,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS10062-4248STDY7309133,VBS10062-4248STDY7309133,16042,Brandy St. Laurent,Cambodia,Thmar Da,2011,4,12.155,102.735 +VBS10064-4248STDY7309134,VBS10064-4248STDY7309134,14857,Brandy St. Laurent,Cambodia,Thmar Da,2011,3,12.155,102.735 +VBS16552-4248STDY7309135,VBS16552-4248STDY7309135,KV-21-00482,Brandy St. Laurent,Cambodia,Chean Mok,2014,3,13.770,104.920 +VBS16553-4248STDY7309136,VBS16553-4248STDY7309136,KV-21-00281,Brandy St. Laurent,Cambodia,Chean Mok,2014,3,13.770,104.920 +VBS16555-4248STDY7309137,VBS16555-4248STDY7309137,KV-21-00759,Brandy St. Laurent,Cambodia,Chean Mok,2014,3,13.770,104.920 +VBS16558-4248STDY7309138,VBS16558-4248STDY7309138,KV-21-00805,Brandy St. Laurent,Cambodia,Chean Mok,2014,3,13.770,104.920 +VBS16559-4248STDY7309139,VBS16559-4248STDY7309139,KV-21-00776,Brandy St. Laurent,Cambodia,Chean Mok,2014,3,13.770,104.920 +VBS16592-4248STDY7309143,VBS16592-4248STDY7309143,KV-21-02137,Brandy St. Laurent,Cambodia,Chean Mok,2014,7,13.770,104.920 +VBS16604-4248STDY7309145,VBS16604-4248STDY7309145,KV-22-01026,Brandy St. Laurent,Cambodia,Preah Kleang,2014,10,13.667,104.982 +VBS16619-4248STDY7309146,VBS16619-4248STDY7309146,KV-32-00513,Brandy St. Laurent,Cambodia,Sayas,2014,2,13.548,107.025 +VBS16627-4248STDY7309147,VBS16627-4248STDY7309147,KV-32-01364,Brandy St. Laurent,Cambodia,Sayas,2014,4,13.548,107.025 +VBS16631-4248STDY7309148,VBS16631-4248STDY7309148,KV-32-03516,Brandy St. Laurent,Cambodia,Sayas,2014,9,13.548,107.025 +VBS16646-4248STDY7309149,VBS16646-4248STDY7309149,1635,Brandy St. Laurent,Cambodia,Thmar Da,2010,1,12.155,102.735 +VBS16648-4248STDY7309150,VBS16648-4248STDY7309150,1649,Brandy St. Laurent,Cambodia,Thmar Da,2010,1,12.155,102.735 +VBS16649-4248STDY7309151,VBS16649-4248STDY7309151,1652,Brandy St. Laurent,Cambodia,Thmar Da,2010,1,12.155,102.735 +VBS16650-4248STDY7309152,VBS16650-4248STDY7309152,1658,Brandy St. Laurent,Cambodia,Thmar Da,2010,1,12.155,102.735 +VBS16651-4248STDY7309153,VBS16651-4248STDY7309153,1721,Brandy St. Laurent,Cambodia,Thmar Da,2010,1,12.155,102.735 +VBS16652-4248STDY7309154,VBS16652-4248STDY7309154,1740,Brandy St. Laurent,Cambodia,Thmar Da,2010,1,12.155,102.735 +VBS16654-4248STDY7309155,VBS16654-4248STDY7309155,1972,Brandy St. Laurent,Cambodia,Thmar Da,2010,1,12.155,102.735 +VBS16664-4248STDY7309156,VBS16664-4248STDY7309156,3897,Brandy St. Laurent,Cambodia,Thmar Da,2010,3,12.155,102.735 +VBS16686-4248STDY7309158,VBS16686-4248STDY7309158,4191,Brandy St. Laurent,Cambodia,Thmar Da,2010,2,12.155,102.735 +VBS16694-4248STDY7309160,VBS16694-4248STDY7309160,4399,Brandy St. Laurent,Cambodia,Thmar Da,2010,3,12.155,102.735 +VBS16695-4248STDY7309161,VBS16695-4248STDY7309161,4409,Brandy St. Laurent,Cambodia,Thmar Da,2010,3,12.155,102.735 +VBS16698-4248STDY7309162,VBS16698-4248STDY7309162,4418,Brandy St. Laurent,Cambodia,Thmar Da,2010,3,12.155,102.735 +VBS16703-4248STDY7309163,VBS16703-4248STDY7309163,4626,Brandy St. Laurent,Cambodia,Thmar Da,2010,2,12.155,102.735 +VBS16707-4248STDY7309164,VBS16707-4248STDY7309164,4883,Brandy St. Laurent,Cambodia,Thmar Da,2010,3,12.155,102.735 +VBS16713-4248STDY7309165,VBS16713-4248STDY7309165,4932,Brandy St. Laurent,Cambodia,Thmar Da,2010,3,12.155,102.735 +VBS16724-4248STDY7309166,VBS16724-4248STDY7309166,5051,Brandy St. Laurent,Cambodia,Thmar Da,2010,3,12.155,102.735 +VBS16732-4248STDY7309167,VBS16732-4248STDY7309167,5440,Brandy St. Laurent,Cambodia,Thmar Da,2010,2,12.155,102.735 +VBS16736-4248STDY7309168,VBS16736-4248STDY7309168,5506,Brandy St. Laurent,Cambodia,Thmar Da,2010,2,12.155,102.735 +VBS09376-4248STDY7918389,VBS09376-4248STDY7918389,CB-2-00373,Brandy St. Laurent,Cambodia,Preah Kleang,2016,9,13.667,104.982 +VBS09377-4248STDY7918390,VBS09377-4248STDY7918390,CB-2-00328,Brandy St. Laurent,Cambodia,Preah Kleang,2016,9,13.667,104.982 +VBS09380-4248STDY7918392,VBS09380-4248STDY7918392,CB-2-00466,Brandy St. Laurent,Cambodia,Preah Kleang,2016,9,13.667,104.982 +VBS09381-4248STDY7918393,VBS09381-4248STDY7918393,CB-2-00268,Brandy St. Laurent,Cambodia,Preah Kleang,2016,9,13.667,104.982 +VBS09385-4248STDY7918394,VBS09385-4248STDY7918394,CB-2-00280,Brandy St. Laurent,Cambodia,Preah Kleang,2016,9,13.667,104.982 +VBS09386-4248STDY7918395,VBS09386-4248STDY7918395,CB-2-00372,Brandy St. Laurent,Cambodia,Preah Kleang,2016,10,13.667,104.982 +VBS09389-3429STDY7351727,VBS09389-3429STDY7351727,CB-2-00416,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09390-3429STDY7351728,VBS09390-3429STDY7351728,CB-2-00431,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09392-4248STDY7918396,VBS09392-4248STDY7918396,CB-2-00474,Brandy St. Laurent,Cambodia,Preah Kleang,2016,11,13.667,104.982 +VBS09393-4248STDY7918397,VBS09393-4248STDY7918397,CB-2-00371,Brandy St. Laurent,Cambodia,Preah Kleang,2016,12,13.667,104.982 +VBS09394-4248STDY7918398,VBS09394-4248STDY7918398,CB-2-00453,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09395-4248STDY7918399,VBS09395-4248STDY7918399,CB-2-00036,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09396-4248STDY7918400,VBS09396-4248STDY7918400,CB-2-00357,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09401-4248STDY7918401,VBS09401-4248STDY7918401,CB-2-00362,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09402-4248STDY7918402,VBS09402-4248STDY7918402,CB-2-00374,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09403-3429STDY7351725,VBS09403-3429STDY7351725,CB-2-00212,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09404-4248STDY7918405,VBS09404-4248STDY7918405,CB-2-00472,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09405-4248STDY7918406,VBS09405-4248STDY7918406,CB-2-00283,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09406-4248STDY7918407,VBS09406-4248STDY7918407,CB-2-00116,Brandy St. Laurent,Cambodia,Preah Kleang,2016,3,13.667,104.982 +VBS09449-4248STDY7918414,VBS09449-4248STDY7918414,CB-2-00908,Brandy St. Laurent,Cambodia,Preah Kleang,2016,6,13.667,104.982 +VBS09486-4248STDY7918429,VBS09486-4248STDY7918429,CB-2-03806,Brandy St. Laurent,Cambodia,Preah Kleang,2016,2,13.667,104.982 +VBS09510-4248STDY7918433,VBS09510-4248STDY7918433,CB-2-05191,Brandy St. Laurent,Cambodia,Preah Kleang,2016,1,13.667,104.982 +VBS09512-4248STDY7918434,VBS09512-4248STDY7918434,CB-2-05084,Brandy St. Laurent,Cambodia,Preah Kleang,2016,2,13.667,104.982 +VBS09522-4248STDY7918438,VBS09522-4248STDY7918438,CB-2-05467,Brandy St. Laurent,Cambodia,Preah Kleang,2016,4,13.667,104.982 +VBS09523-4248STDY7918439,VBS09523-4248STDY7918439,CB-2-05257,Brandy St. Laurent,Cambodia,Preah Kleang,2016,4,13.667,104.982 +VBS09526-4248STDY7918440,VBS09526-4248STDY7918440,KV-21-01130,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09530-4248STDY7918441,VBS09530-4248STDY7918441,KV-21-00533,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09533-4248STDY7918442,VBS09533-4248STDY7918442,KV-21-01077,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09543-4248STDY7918445,VBS09543-4248STDY7918445,KV-22-00580,Brandy St. Laurent,Cambodia,Preah Kleang,2014,6,13.667,104.982 +VBS09544-4248STDY7918446,VBS09544-4248STDY7918446,KV-22-00035,Brandy St. Laurent,Cambodia,Preah Kleang,2014,6,13.667,104.982 +VBS09550-4248STDY7918447,VBS09550-4248STDY7918447,KV-22-00489,Brandy St. Laurent,Cambodia,Preah Kleang,2014,7,13.667,104.982 +VBS09578-4248STDY7918455,VBS09578-4248STDY7918455,KV-21-01491,Brandy St. Laurent,Cambodia,Chean Mok,2014,8,13.770,104.920 +VBS09584-3429STDY7351712,VBS09584-3429STDY7351712,KV-21-01465,Brandy St. Laurent,Cambodia,Chean Mok,2014,6,13.770,104.920 +VBS09592-4248STDY7918457,VBS09592-4248STDY7918457,KV-21-01645,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09594-4248STDY7918458,VBS09594-4248STDY7918458,KV-21-00860,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09604-4248STDY7918460,VBS09604-4248STDY7918460,KV-22-00648,Brandy St. Laurent,Cambodia,Preah Kleang,2014,12,13.667,104.982 +VBS09664-4248STDY7918477,VBS09664-4248STDY7918477,KV-21-02326,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09665-4248STDY7918478,VBS09665-4248STDY7918478,KV-21-02352,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09667-4248STDY7918480,VBS09667-4248STDY7918480,KV-21-02332,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09668-4248STDY7918481,VBS09668-4248STDY7918481,KV-21-02375,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09669-4248STDY7918482,VBS09669-4248STDY7918482,KV-21-02396,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09670-4248STDY7918483,VBS09670-4248STDY7918483,KV-21-02446,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09671-4248STDY7918484,VBS09671-4248STDY7918484,KV-21-02382,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS09682-4248STDY7918485,VBS09682-4248STDY7918485,KV-22-00470,Brandy St. Laurent,Cambodia,Preah Kleang,2014,12,13.667,104.982 +VBS09683-4248STDY7918486,VBS09683-4248STDY7918486,KV-22-01667,Brandy St. Laurent,Cambodia,Preah Kleang,2014,12,13.667,104.982 +VBS09688-4248STDY7918489,VBS09688-4248STDY7918489,KV-22-01141,Brandy St. Laurent,Cambodia,Preah Kleang,2014,10,13.667,104.982 +VBS09700-4248STDY7918492,VBS09700-4248STDY7918492,KV-21-02947,Brandy St. Laurent,Cambodia,Chean Mok,2014,11,13.770,104.920 +VBS09706-4248STDY7918495,VBS09706-4248STDY7918495,KV-21-03577,Brandy St. Laurent,Cambodia,Chean Mok,2014,12,13.770,104.920 +VBS09732-4248STDY7918503,VBS09732-4248STDY7918503,KV-21-02974,Brandy St. Laurent,Cambodia,Chean Mok,2015,1,13.770,104.920 +VBS09733-4248STDY7918504,VBS09733-4248STDY7918504,KV-21-03830,Brandy St. Laurent,Cambodia,Chean Mok,2015,1,13.770,104.920 +VBS09742-4248STDY7918506,VBS09742-4248STDY7918506,KV-21-02796,Brandy St. Laurent,Cambodia,Chean Mok,2015,1,13.770,104.920 +VBS09749-4248STDY7918510,VBS09749-4248STDY7918510,KV-22-00873,Brandy St. Laurent,Cambodia,Preah Kleang,2015,1,13.667,104.982 +VBS09750-4248STDY7918512,VBS09750-4248STDY7918512,KV-22-00988,Brandy St. Laurent,Cambodia,Preah Kleang,2015,1,13.667,104.982 +VBS09751-4248STDY7918513,VBS09751-4248STDY7918513,KV-22-01139,Brandy St. Laurent,Cambodia,Preah Kleang,2015,1,13.667,104.982 +VBS09752-4248STDY7918514,VBS09752-4248STDY7918514,KV-22-01532,Brandy St. Laurent,Cambodia,Preah Kleang,2015,1,13.667,104.982 +VBS09753-4248STDY7918515,VBS09753-4248STDY7918515,KV-22-01120,Brandy St. Laurent,Cambodia,Preah Kleang,2015,1,13.667,104.982 +VBS09754-4248STDY7918516,VBS09754-4248STDY7918516,KV-22-01641,Brandy St. Laurent,Cambodia,Preah Kleang,2015,1,13.667,104.982 +VBS09755-4248STDY7918517,VBS09755-4248STDY7918517,KV-21-00276,Brandy St. Laurent,Cambodia,Chean Mok,2014,8,13.770,104.920 +VBS09757-4248STDY7918518,VBS09757-4248STDY7918518,KV-21-00230,Brandy St. Laurent,Cambodia,Chean Mok,2014,8,13.770,104.920 +VBS09763-4248STDY7918519,VBS09763-4248STDY7918519,KV-21-00757,Brandy St. Laurent,Cambodia,Chean Mok,2014,9,13.770,104.920 +VBS09764-4248STDY7918520,VBS09764-4248STDY7918520,KV-21-01172,Brandy St. Laurent,Cambodia,Chean Mok,2014,9,13.770,104.920 +VBS09766-4248STDY7918521,VBS09766-4248STDY7918521,KV-31-03722,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09767-4248STDY7918522,VBS09767-4248STDY7918522,KV-31-03654,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09774-4248STDY7918524,VBS09774-4248STDY7918524,KV-31-04664,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09779-4248STDY7918526,VBS09779-4248STDY7918526,KV-32-04581,Brandy St. Laurent,Cambodia,Sayas,2015,1,13.548,107.025 +VBS09780-4248STDY7918527,VBS09780-4248STDY7918527,KV-32-04572,Brandy St. Laurent,Cambodia,Sayas,2015,1,13.548,107.025 +VBS09784-4248STDY7918528,VBS09784-4248STDY7918528,KV-31-04653,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09788-4248STDY7918530,VBS09788-4248STDY7918530,KV-31-04789,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09789-4248STDY7918531,VBS09789-4248STDY7918531,KV-32-04537,Brandy St. Laurent,Cambodia,Sayas,2015,1,13.548,107.025 +VBS09793-4248STDY7918532,VBS09793-4248STDY7918532,KV-32-01098,Brandy St. Laurent,Cambodia,Sayas,2014,6,13.548,107.025 +VBS09796-4248STDY7918534,VBS09796-4248STDY7918534,KV-32-01327,Brandy St. Laurent,Cambodia,Sayas,2014,7,13.548,107.025 +VBS09804-3429STDY7351716,VBS09804-3429STDY7351716,KV-31-00536,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09805-4248STDY7918537,VBS09805-4248STDY7918537,KV-31-00248,Brandy St. Laurent,Cambodia,Chamkar San,2014,2,13.595,106.995 +VBS09806-4248STDY7918538,VBS09806-4248STDY7918538,KV-31-00208,Brandy St. Laurent,Cambodia,Chamkar San,2014,2,13.595,106.995 +VBS09813-4248STDY7918539,VBS09813-4248STDY7918539,KV-31-00505,Brandy St. Laurent,Cambodia,Chamkar San,2014,3,13.595,106.995 +VBS09820-4248STDY7918542,VBS09820-4248STDY7918542,KV-31-00848,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09822-3429STDY7351713,VBS09822-3429STDY7351713,KV-31-00730,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09824-3429STDY7351714,VBS09824-3429STDY7351714,KV-31-00852,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09825-3429STDY7351715,VBS09825-3429STDY7351715,KV-31-00624,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09826-4248STDY7918544,VBS09826-4248STDY7918544,KV-31-00872,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09828-4248STDY7918545,VBS09828-4248STDY7918545,KV-31-00691,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09830-4248STDY7918546,VBS09830-4248STDY7918546,KV-31-00888,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09831-4248STDY7918547,VBS09831-4248STDY7918547,KV-32-01357,Brandy St. Laurent,Cambodia,Sayas,2014,5,13.548,107.025 +VBS09834-4248STDY7918548,VBS09834-4248STDY7918548,KV-32-01423,Brandy St. Laurent,Cambodia,Sayas,2014,6,13.548,107.025 +VBS09835-4248STDY7918549,VBS09835-4248STDY7918549,KV-32-01545,Brandy St. Laurent,Cambodia,Sayas,2014,6,13.548,107.025 +VBS09837-4248STDY7918550,VBS09837-4248STDY7918550,KV-32-01550,Brandy St. Laurent,Cambodia,Sayas,2014,6,13.548,107.025 +VBS09838-4248STDY7918551,VBS09838-4248STDY7918551,KV-32-01360,Brandy St. Laurent,Cambodia,Sayas,2014,6,13.548,107.025 +VBS09840-4248STDY7918552,VBS09840-4248STDY7918552,KV-32-01406,Brandy St. Laurent,Cambodia,Sayas,2014,6,13.548,107.025 +VBS09841-4248STDY7918553,VBS09841-4248STDY7918553,KV-32-01405,Brandy St. Laurent,Cambodia,Sayas,2014,6,13.548,107.025 +VBS09842-4248STDY7918554,VBS09842-4248STDY7918554,KV-32-01384,Brandy St. Laurent,Cambodia,Sayas,2014,6,13.548,107.025 +VBS09844-4248STDY7918555,VBS09844-4248STDY7918555,KV-32-01858,Brandy St. Laurent,Cambodia,Sayas,2014,7,13.548,107.025 +VBS09847-4248STDY7918558,VBS09847-4248STDY7918558,KV-32-01864,Brandy St. Laurent,Cambodia,Sayas,2014,7,13.548,107.025 +VBS09849-4248STDY7918560,VBS09849-4248STDY7918560,KV-32-01873,Brandy St. Laurent,Cambodia,Sayas,2014,7,13.548,107.025 +VBS09853-4248STDY7918561,VBS09853-4248STDY7918561,KV-31-01264,Brandy St. Laurent,Cambodia,Chamkar San,2014,10,13.595,106.995 +VBS09855-4248STDY7918562,VBS09855-4248STDY7918562,KV-31-01330,Brandy St. Laurent,Cambodia,Chamkar San,2014,10,13.595,106.995 +VBS09857-4248STDY7918564,VBS09857-4248STDY7918564,KV-31-01373,Brandy St. Laurent,Cambodia,Chamkar San,2014,10,13.595,106.995 +VBS09862-4248STDY7918566,VBS09862-4248STDY7918566,KV-31-01239,Brandy St. Laurent,Cambodia,Chamkar San,2014,10,13.595,106.995 +VBS09865-4248STDY7918569,VBS09865-4248STDY7918569,KV-31-01258,Brandy St. Laurent,Cambodia,Chamkar San,2014,10,13.595,106.995 +VBS09872-4248STDY7918571,VBS09872-4248STDY7918571,KV-31-01346,Brandy St. Laurent,Cambodia,Chamkar San,2014,11,13.595,106.995 +VBS09874-4248STDY7918572,VBS09874-4248STDY7918572,KV-31-01462,Brandy St. Laurent,Cambodia,Chamkar San,2014,12,13.595,106.995 +VBS09875-4248STDY7918573,VBS09875-4248STDY7918573,KV-31-01573,Brandy St. Laurent,Cambodia,Chamkar San,2014,12,13.595,106.995 +VBS09878-4248STDY7918575,VBS09878-4248STDY7918575,KV-31-01461,Brandy St. Laurent,Cambodia,Chamkar San,2014,12,13.595,106.995 +VBS09898-4248STDY7918582,VBS09898-4248STDY7918582,KV-31-01807,Brandy St. Laurent,Cambodia,Chamkar San,2014,4,13.595,106.995 +VBS09912-4248STDY7918589,VBS09912-4248STDY7918589,KV-31-02263,Brandy St. Laurent,Cambodia,Chamkar San,2014,7,13.595,106.995 +VBS09914-3429STDY7351719,VBS09914-3429STDY7351719,KV-31-02166,Brandy St. Laurent,Cambodia,Chamkar San,2014,9,13.595,106.995 +VBS09927-3429STDY7351720,VBS09927-3429STDY7351720,KV-31-02522,Brandy St. Laurent,Cambodia,Chamkar San,2014,10,13.595,106.995 +VBS09932-3429STDY7351721,VBS09932-3429STDY7351721,KV-32-05072,Brandy St. Laurent,Cambodia,Sayas,2014,10,13.548,107.025 +VBS09950-4248STDY7918611,VBS09950-4248STDY7918611,KV-31-03177,Brandy St. Laurent,Cambodia,Chamkar San,2014,8,13.595,106.995 +VBS09951-4248STDY7918612,VBS09951-4248STDY7918612,KV-31-03267,Brandy St. Laurent,Cambodia,Chamkar San,2014,8,13.595,106.995 +VBS09954-4248STDY7918613,VBS09954-4248STDY7918613,KV-32-04036,Brandy St. Laurent,Cambodia,Sayas,2014,10,13.548,107.025 +VBS09956-4248STDY7918614,VBS09956-4248STDY7918614,KV-32-03876,Brandy St. Laurent,Cambodia,Sayas,2014,10,13.548,107.025 +VBS09959-4248STDY7918615,VBS09959-4248STDY7918615,KV-32-03844,Brandy St. Laurent,Cambodia,Sayas,2014,10,13.548,107.025 +VBS09968-4248STDY7918619,VBS09968-4248STDY7918619,KV-32-04372,Brandy St. Laurent,Cambodia,Sayas,2014,12,13.548,107.025 +VBS09976-4248STDY7918620,VBS09976-4248STDY7918620,KV-31-03352,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09978-4248STDY7918622,VBS09978-4248STDY7918622,KV-31-03602,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09980-4248STDY7918623,VBS09980-4248STDY7918623,KV-31-03536,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09982-4248STDY7918625,VBS09982-4248STDY7918625,KV-31-03479,Brandy St. Laurent,Cambodia,Chamkar San,2015,1,13.595,106.995 +VBS09983-4248STDY7918626,VBS09983-4248STDY7918626,KV-31-01500,Brandy St. Laurent,Cambodia,Chamkar San,2014,11,13.595,106.995 +VBS16554-4248STDY7918627,VBS16554-4248STDY7918627,KV-21-00426,Brandy St. Laurent,Cambodia,Chean Mok,2014,8,13.770,104.920 +VBS16556-4248STDY7918628,VBS16556-4248STDY7918628,KV-21-00539,Brandy St. Laurent,Cambodia,Chean Mok,2014,9,13.770,104.920 +VBS16563-4248STDY7918631,VBS16563-4248STDY7918631,KV-21-01094,Brandy St. Laurent,Cambodia,Chean Mok,2014,10,13.770,104.920 +VBS16568-4248STDY7918632,VBS16568-4248STDY7918632,KV-21-01815,Brandy St. Laurent,Cambodia,Chean 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+VBS16626-4248STDY7918669,https://1175-vo-kh-stlaurent-minimus.cog.sanger.ac.uk/VBS16626-4248STDY7918669-2019-07-21.bam,,https://1175-vo-kh-stlaurent-minimus.cog.sanger.ac.uk/VBS16626-4248STDY7918669-2019-07-22.vcf.gz,,,, +VBS16628-4248STDY7918670,https://1175-vo-kh-stlaurent-minimus.cog.sanger.ac.uk/VBS16628-4248STDY7918670-2019-07-22.bam,,https://1175-vo-kh-stlaurent-minimus.cog.sanger.ac.uk/VBS16628-4248STDY7918670-2019-07-22.vcf.gz,,,, +VBS16630-4248STDY7918671,https://1175-vo-kh-stlaurent-minimus.cog.sanger.ac.uk/VBS16630-4248STDY7918671-2019-07-22.bam,,https://1175-vo-kh-stlaurent-minimus.cog.sanger.ac.uk/VBS16630-4248STDY7918671-2019-07-22.vcf.gz,,,, diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/samples.meta.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/samples.meta.csv index f10d3bef8..f56c518e6 100644 --- a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/samples.meta.csv +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/samples.meta.csv @@ -1,48 +1,48 @@ -sample_id,partner_sample_id,contributor,country,location,year,month,latitude,longitude,sex_call -VBS46299-6321STDY9453299,158,Shiaful Alam,Bangladesh,Bangladesh_2,2018,5,22.287,92.194,UKN -VBS46307-6321STDY9453307,2973,Shiaful Alam,Bangladesh,Bangladesh_1,2018,6,22.254,92.203,UKN -VBS46315-6321STDY9453315,2340,Shiaful Alam,Bangladesh,Bangladesh_1,2018,7,22.254,92.203,UKN -VBS46323-6321STDY9453323,2525,Shiaful Alam,Bangladesh,Bangladesh_2,2018,7,22.287,92.194,UKN -VBS46331-6321STDY9453331,5249,Shiaful Alam,Bangladesh,Bangladesh_1,2018,9,22.254,92.203,UKN -VBS46339-6321STDY9453339,4417,Shiaful Alam,Bangladesh,Bangladesh_4,2018,9,22.245,92.288,UKN -VBS46300-6321STDY9453300,1473,Shiaful 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-VBS46341-6321STDY9453341,4624,Shiaful Alam,Bangladesh,Bangladesh_3,2018,10,22.382,92.282,UKN -VBS46302-6321STDY9453302,240,Shiaful Alam,Bangladesh,Bangladesh_4,2018,6,22.245,92.288,UKN -VBS46310-6321STDY9453310,3097,Shiaful Alam,Bangladesh,Bangladesh_3,2018,6,22.382,92.282,UKN -VBS46318-6321STDY9453318,2349,Shiaful Alam,Bangladesh,Bangladesh_1,2018,7,22.254,92.203,UKN -VBS46326-6321STDY9453326,3225,Shiaful Alam,Bangladesh,Bangladesh_1,2018,8,22.254,92.203,UKN -VBS46334-6321STDY9453334,6485,Shiaful Alam,Bangladesh,Bangladesh_3,2018,9,22.382,92.282,UKN -VBS46342-6321STDY9453342,4629,Shiaful Alam,Bangladesh,Bangladesh_3,2018,10,22.382,92.282,UKN -VBS46303-6321STDY9453303,259,Shiaful Alam,Bangladesh,Bangladesh_4,2018,6,22.245,92.288,UKN -VBS46311-6321STDY9453311,1725,Shiaful Alam,Bangladesh,Bangladesh_2,2018,6,22.287,92.194,UKN -VBS46319-6321STDY9453319,2474,Shiaful Alam,Bangladesh,Bangladesh_2,2018,7,22.287,92.194,UKN -VBS46327-6321STDY9453327,5587,Shiaful 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-VBS46321-6321STDY9453321,2500,Shiaful Alam,Bangladesh,Bangladesh_2,2018,7,22.287,92.194,UKN -VBS46329-6321STDY9453329,5809,Shiaful Alam,Bangladesh,Bangladesh_4,2018,8,22.245,92.288,UKN -VBS46337-6321STDY9453337,6454,Shiaful Alam,Bangladesh,Bangladesh_3,2018,9,22.382,92.282,UKN -VBS46345-6321STDY9453345,1211,Shiaful Alam,Bangladesh,Bangladesh_1,2018,5,22.254,92.203,UKN -VBS46306-6321STDY9453306,2972,Shiaful Alam,Bangladesh,Bangladesh_1,2018,6,22.254,92.203,UKN -VBS46314-6321STDY9453314,2328,Shiaful Alam,Bangladesh,Bangladesh_1,2018,7,22.254,92.203,UKN -VBS46322-6321STDY9453322,2524,Shiaful Alam,Bangladesh,Bangladesh_2,2018,7,22.287,92.194,UKN -VBS46330-6321STDY9453330,5246,Shiaful Alam,Bangladesh,Bangladesh_1,2018,9,22.254,92.203,UKN +sample_id,partner_sample_id,contributor,country,location,year,month,latitude,longitude,sex_call +VBS46299-6321STDY9453299,158,Shiaful Alam,Bangladesh,Bangladesh_2,2018,5,22.287,92.194,UKN +VBS46307-6321STDY9453307,2973,Shiaful 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+VBS46345-6321STDY9453345,67.62,68,69,69.4,70,71,75.11,75,75,71.31,39,250,37.02,31,30,60.14,63,63,79.29,78,74,81.78,55,250,65.89,68,5,74.79,61,2,53.74,47,2,99.31,104,250,85.17,85,82,64.04,65,66,40.71,41,2,53.28,41,5,56.48,48,3,68.76,72,75,51.1,33,250,85.14,57,250,48.82,50,3,134.13,142,250,126.68,88,250,65.45,67,69,111.4,80,250,58.1,56,2,134.55,126,250,75.56,47,250,61.15,63,67,72.55,61,250,81.61,44,250,157.89,198,250,223.95,250,250,107.91,67,250,63.79,66,67,74.13,73,69,62.86,61,68,58.69,53,250,67.04,53,2,78.62,54,250,52.02,51,57,68.01,59,250,40.35,39,42,49.17,50,71,53.77,59,61,65.34,67,68,49.0,50,72,46.7,46,33,52.11,41,7,51.85,37,2,56.5,61,60,55.03,32,2,62.65,50,250,113.6,105,250,66.46,53,2,53.61,56,59,68.97,70,71,54.14,58,63,43.21,41,27,83.66,42,250,62.93,68,73,76.73,65,5,59.09,38,250,54.5,57,62,138.05,157,250,70.83,24,250,71.3,72,74,78.57,41,250,17.54,10,3,118.9,68,250,69.76,55,250,74.97,52,25,127.62,144,250,63.9,41,2,103.27,59,250,64.39,66,67,64.52,59,61,101.35,58,250,46.61,47,50,66.65,35,250,128.03,103,250,65.48,67,68,95.17,57,250,144.74,172,250,110.35,62,250,68.93,70,71,49.02,52,57,107.18,87,250,68.49,69,70,64.78,66,68,81.66,51,250,55.34,56,2,156.6,217,250,64.01,65,66,108.82,98,250,66.77,66,67,55.48,22,2,67.99,34,5,103.89,81,250,42.08,24,8,64.5,66,67,66.19,39,22,155.44,205,250,63.78,65,65,72.78,45,26,79.69,70,60,62.26,64,64,84.04,92,111,40.09,39,41,65.04,64,66,63.32,65,67,91.09,46,250,59.54,63,65,51.26,57,60,66.48,66,67,76.25,68,3,71.95,72,72,63.73,65,66,64.14,66,66,118.78,133,250,63.57,64,65,62.81,63,63,63.04,62,64,67.24,49,9,127.05,80,250,67.87,68,68,63.54,57,2,75.09,75,75,64.85,66,67,63.6,64,65,43.79,26,20,76.16,76,77,63.35,65,66,66.42,66,65,64.26,66,67,60.81,61,63,68.7,65,66,53.9,59,73,70.35,72,73,224.92,250,250,59.38,61,61,65.13,66,65,57.38,60,62,66.77,67,65,8.65,8,2,67.49,67,67,68.14,69,70,63.09,64,64,61.1,62,63,62.27,61,64,96.13,57,250,63.5,62,64,62.54,65,66,60.86,58,67,61.54,61,61,63.49,66,66,102.13,51,250,68.92,70,70,66.66,61,250,65.08,66,69,71.27,68,71,62.52,65,66,64.6,60,62,59.9,59,64,75.53,40,250,62.05,63,64,57.54,60,64,65.36,64,64,71.06,71,72,61.4,60,60,109.43,91,250,71.67,53,250,99.26,80,250,50.38,44,3,67.51,59,250,76.06,77,77,60.36,60,63,95.24,43,250,99.46,101,106,65.53,67,68,78.18,45,250,65.27,44,250,67.97,68,71,76.84,57,250,67.29,42,250,63.29,41,2,55.16,56,60,64.28,61,61,100.91,63,250,61.17,59,56,66.77,68,69,76.12,56,250,97.93,72,250,64.74,65,66,83.71,39,250,134.24,133,250,75.81,49,250,65.09,60,62,45.6,36,5,51.95,51,60,122.8,131,250,0.948,0.03438 diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv index d7514da1a..4d6f16f4e 100644 --- a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1276-AD-BD-ALAM-VMF00156/wgs_accession_data.csv @@ -1,48 +1,48 @@ -sample_id,run_ena -VBS46299-6321STDY9453299,"ERR5967855, ERR5967879, ERR5967903" -VBS46300-6321STDY9453300,"ERR5967861, ERR5967885, ERR5967909" -VBS46301-6321STDY9453301,"ERR5967867, ERR5967891, ERR5967915" -VBS46302-6321STDY9453302,"ERR5967873, ERR5967897, ERR5967921" -VBS46303-6321STDY9453303,"ERR6045486, ERR6045509, ERR6045532" -VBS46304-6321STDY9453304,"ERR6045492, ERR6045515, ERR6045538" -VBS46305-6321STDY9453305,"ERR6045498, ERR6045521, ERR6045544" -VBS46306-6321STDY9453306,"ERR6045504, ERR6045527, ERR6045550" -VBS46307-6321STDY9453307,"ERR5967856, ERR5967880, ERR5967904" -VBS46308-6321STDY9453308,"ERR5967862, ERR5967886, ERR5967910" -VBS46309-6321STDY9453309,"ERR5967868, ERR5967892, ERR5967916" -VBS46310-6321STDY9453310,"ERR5967874, ERR5967898, ERR5967922" -VBS46311-6321STDY9453311,"ERR6045487, ERR6045510, ERR6045533" -VBS46312-6321STDY9453312,"ERR6045493, ERR6045516, ERR6045539" -VBS46313-6321STDY9453313,"ERR6045499, ERR6045522, ERR6045545" -VBS46314-6321STDY9453314,"ERR6045505, ERR6045528, ERR6045551" -VBS46315-6321STDY9453315,"ERR5967857, ERR5967881, ERR5967905" -VBS46316-6321STDY9453316,"ERR5967863, ERR5967887, ERR5967911" -VBS46317-6321STDY9453317,"ERR5967869, ERR5967893, ERR5967917" -VBS46318-6321STDY9453318,"ERR5967875, ERR5967899, ERR5967923" -VBS46319-6321STDY9453319,"ERR6045488, ERR6045511, ERR6045534" -VBS46320-6321STDY9453320,"ERR6045494, ERR6045517, ERR6045540" -VBS46321-6321STDY9453321,"ERR6045500, ERR6045523, ERR6045546" -VBS46322-6321STDY9453322,"ERR6045506, ERR6045529, ERR6045552" -VBS46323-6321STDY9453323,"ERR5967858, ERR5967882, ERR5967906" -VBS46324-6321STDY9453324,"ERR5967864, ERR5967888, ERR5967912" -VBS46325-6321STDY9453325,"ERR5967870, ERR5967894, ERR5967918" -VBS46326-6321STDY9453326,"ERR5967876, ERR5967900, ERR5967924" -VBS46327-6321STDY9453327,"ERR6045489, ERR6045512, ERR6045535" -VBS46328-6321STDY9453328,"ERR6045495, ERR6045518, ERR6045541" -VBS46329-6321STDY9453329,"ERR6045501, ERR6045524, ERR6045547" -VBS46330-6321STDY9453330,"ERR6045507, ERR6045530, ERR6045553" -VBS46331-6321STDY9453331,"ERR5967859, ERR5967883, ERR5967907" -VBS46332-6321STDY9453332,"ERR5967865, ERR5967889, ERR5967913" -VBS46333-6321STDY9453333,"ERR5967871, ERR5967895, ERR5967919" -VBS46334-6321STDY9453334,"ERR5967877, ERR5967901, ERR5967925" -VBS46335-6321STDY9453335,"ERR6045490, ERR6045513, ERR6045536" -VBS46336-6321STDY9453336,"ERR6045496, ERR6045519, ERR6045542" -VBS46337-6321STDY9453337,"ERR6045502, ERR6045525, ERR6045548" -VBS46338-6321STDY9453338,"ERR6045508, ERR6045531, ERR6045554" -VBS46339-6321STDY9453339,"ERR5967860, ERR5967884, ERR5967908" -VBS46340-6321STDY9453340,"ERR5967866, ERR5967890, ERR5967914" -VBS46341-6321STDY9453341,"ERR5967872, ERR5967896, ERR5967920" -VBS46342-6321STDY9453342,"ERR5967878, ERR5967902, ERR5967926" -VBS46343-6321STDY9453343,"ERR6045491, ERR6045514, ERR6045537" -VBS46344-6321STDY9453344,"ERR6045497, ERR6045520, ERR6045543" -VBS46345-6321STDY9453345,"ERR6045503, ERR6045526, ERR6045549" +sample_id,run_ena,analysis_ena +VBS46299-6321STDY9453299,, +VBS46300-6321STDY9453300,, +VBS46301-6321STDY9453301,, +VBS46302-6321STDY9453302,, +VBS46303-6321STDY9453303,, +VBS46304-6321STDY9453304,, +VBS46305-6321STDY9453305,, +VBS46306-6321STDY9453306,, +VBS46307-6321STDY9453307,, +VBS46308-6321STDY9453308,, +VBS46309-6321STDY9453309,, +VBS46310-6321STDY9453310,, +VBS46311-6321STDY9453311,, +VBS46312-6321STDY9453312,, +VBS46313-6321STDY9453313,, +VBS46314-6321STDY9453314,, +VBS46315-6321STDY9453315,, +VBS46316-6321STDY9453316,, +VBS46317-6321STDY9453317,, +VBS46318-6321STDY9453318,, +VBS46319-6321STDY9453319,, +VBS46320-6321STDY9453320,, +VBS46321-6321STDY9453321,, +VBS46322-6321STDY9453322,, +VBS46323-6321STDY9453323,, +VBS46324-6321STDY9453324,, +VBS46325-6321STDY9453325,, +VBS46326-6321STDY9453326,, +VBS46327-6321STDY9453327,, +VBS46328-6321STDY9453328,, +VBS46329-6321STDY9453329,, +VBS46330-6321STDY9453330,, +VBS46331-6321STDY9453331,, +VBS46332-6321STDY9453332,, +VBS46333-6321STDY9453333,, +VBS46334-6321STDY9453334,, +VBS46335-6321STDY9453335,, +VBS46336-6321STDY9453336,, +VBS46337-6321STDY9453337,, +VBS46338-6321STDY9453338,, +VBS46339-6321STDY9453339,, +VBS46340-6321STDY9453340,, +VBS46341-6321STDY9453341,, +VBS46342-6321STDY9453342,, +VBS46343-6321STDY9453343,, +VBS46344-6321STDY9453344,, +VBS46345-6321STDY9453345,, diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv index c5514f4cc..d6e5988ac 100644 --- a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/sequence_qc_stats.csv @@ -1,27 +1,27 @@ -sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence -VBS45687-6143STDY8787412,32.18,32,32,32.03,32,32,32.37,32,32,32.26,32,32,32.16,32,32,32.07,32,31,0.983,0.01374 -VBS45688-6143STDY8787413,33.19,33,33,33,33,33,33.35,33,33,33.27,33,33,33.24,33,33,33.14,33,33,0.984,0.01378 -VBS45689-6143STDY8787414,34.26,34,34,34.05,34,34,34.53,34,34,34.29,34,34,34.26,34,34,34.19,34,33,0.984,0.01378 -VBS45690-6143STDY8787415,33.07,33,33,32.91,33,33,33.32,33,33,33.19,33,33,33,33,33,32.89,33,33,0.984,0.01377 -VBS45691-6143STDY8787416,34.81,35,34,34.77,35,34,35.02,35,34,35.07,35,35,34.36,34,35,34.7,35,35,0.984,0.01377 -VBS45692-6143STDY8787417,31.07,31,31,30.85,31,31,31.24,31,31,31.11,31,31,31.13,31,31,31.14,31,31,0.983,0.01377 -VBS45701-6143STDY8787420,9.96,9,9,9.91,9,9,10.07,9,9,9.94,9,9,9.91,9,9,9.96,9,9,0.981,0.01546 -VBS45702-6143STDY8787421,8.77,8,8,8.76,8,8,8.81,8,8,8.85,8,8,8.67,8,8,8.74,8,8,0.981,0.01543 -VBS45708-6143STDY8787424,10.22,10,9,10.23,10,9,10.32,10,9,10.38,10,9,9.9,9,9,10.19,10,9,0.981,0.01538 -VBS45709-6143STDY8787425,8.32,8,7,8.31,8,7,8.43,8,7,8.4,8,7,8.1,7,7,8.29,8,7,0.98,0.01539 -VBS45711-6143STDY8787426,9.93,9,9,9.94,9,9,10.05,9,9,10.06,9,9,9.62,9,9,9.88,9,9,0.982,0.01536 -VBS45713-6143STDY8787427,23.63,23,23,23.54,23,23,23.78,23,23,23.77,23,23,23.41,23,23,23.64,23,23,0.983,0.01382 -VBS45717-6143STDY8787429,34.14,34,34,33.83,34,34,34.26,34,34,34.18,34,34,34.39,34,34,34.19,34,34,0.984,0.01375 -VBS45718-6143STDY8787430,35.17,35,35,34.87,35,35,35.34,35,35,35.21,35,35,35.29,35,35,35.26,35,35,0.984,0.01387 -VBS45720-6143STDY8787431,38.61,38,38,38.39,38,38,38.81,39,38,38.61,39,38,38.61,39,38,38.71,39,39,0.984,0.0138 -VBS45723-6143STDY8787432,39.79,40,40,39.73,40,40,40.05,40,40,40.21,40,40,39.09,39,39,39.73,40,40,0.984,0.01373 -VBS45724-6143STDY8787433,34.51,34,34,34.28,34,34,34.63,34,34,34.74,35,34,34.46,34,34,34.51,34,34,0.984,0.01378 -VBS45728-6143STDY8787434,49.49,49,49,49.16,49,49,49.6,49,49,49.69,50,50,49.47,50,50,49.73,50,49,0.984,0.0138 -VBS45734-6143STDY8787435,33.45,33,33,33.27,33,33,33.67,33,33,33.43,33,33,33.65,33,33,33.23,33,33,0.984,0.01379 -VBS45735-6143STDY8787436,33.51,33,33,33.25,33,33,33.58,33,33,33.75,34,33,33.47,33,33,33.7,34,33,0.984,0.01378 -VBS45737-6143STDY8787437,38.95,39,39,38.77,39,38,39.12,39,39,39.23,39,39,38.87,39,39,38.77,39,38,0.984,0.01379 -VBS45738-6143STDY8787438,39.63,40,39,39.44,39,39,39.84,40,39,39.87,40,39,39.46,39,39,39.57,39,39,0.984,0.01378 -VBS45739-6143STDY8787439,38.75,39,38,38.43,38,38,39.04,39,39,38.71,39,38,39.04,39,39,38.59,38,38,0.984,0.01376 -VBS45742-6143STDY8787440,43.47,43,43,43.37,43,44,43.52,43,43,43.55,43,43,43.32,43,43,43.61,43,43,0.984,0.01376 -VBS45743-6143STDY8787441,41.01,41,41,41,41,41,41.3,41,41,41.51,41,41,40.23,40,40,40.81,41,41,0.984,0.01376 +sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence +VBS45687-6143STDY8787412,32.18,32,32,32.03,32,32,32.37,32,32,32.26,32,32,32.16,32,32,32.07,32,31,0.983,0.01374 +VBS45688-6143STDY8787413,33.19,33,33,33.0,33,33,33.35,33,33,33.27,33,33,33.24,33,33,33.14,33,33,0.984,0.01378 +VBS45689-6143STDY8787414,34.26,34,34,34.05,34,34,34.53,34,34,34.29,34,34,34.26,34,34,34.19,34,33,0.984,0.01378 +VBS45690-6143STDY8787415,33.07,33,33,32.91,33,33,33.32,33,33,33.19,33,33,33.0,33,33,32.89,33,33,0.984,0.01377 +VBS45691-6143STDY8787416,34.81,35,34,34.77,35,34,35.02,35,34,35.07,35,35,34.36,34,35,34.7,35,35,0.984,0.01377 +VBS45692-6143STDY8787417,31.07,31,31,30.85,31,31,31.24,31,31,31.11,31,31,31.13,31,31,31.14,31,31,0.983,0.01377 +VBS45701-6143STDY8787420,9.96,9,9,9.91,9,9,10.07,9,9,9.94,9,9,9.91,9,9,9.96,9,9,0.981,0.01546 +VBS45702-6143STDY8787421,8.77,8,8,8.76,8,8,8.81,8,8,8.85,8,8,8.67,8,8,8.74,8,8,0.981,0.01543 +VBS45708-6143STDY8787424,10.22,10,9,10.23,10,9,10.32,10,9,10.38,10,9,9.9,9,9,10.19,10,9,0.981,0.01538 +VBS45709-6143STDY8787425,8.32,8,7,8.31,8,7,8.43,8,7,8.4,8,7,8.1,7,7,8.29,8,7,0.98,0.01539 +VBS45711-6143STDY8787426,9.93,9,9,9.94,9,9,10.05,9,9,10.06,9,9,9.62,9,9,9.88,9,9,0.982,0.01536 +VBS45713-6143STDY8787427,23.63,23,23,23.54,23,23,23.78,23,23,23.77,23,23,23.41,23,23,23.64,23,23,0.983,0.01382 +VBS45717-6143STDY8787429,34.14,34,34,33.83,34,34,34.26,34,34,34.18,34,34,34.39,34,34,34.19,34,34,0.984,0.01375 +VBS45718-6143STDY8787430,35.17,35,35,34.87,35,35,35.34,35,35,35.21,35,35,35.29,35,35,35.26,35,35,0.984,0.01387 +VBS45720-6143STDY8787431,38.61,38,38,38.39,38,38,38.81,39,38,38.61,39,38,38.61,39,38,38.71,39,39,0.984,0.0138 +VBS45723-6143STDY8787432,39.79,40,40,39.73,40,40,40.05,40,40,40.21,40,40,39.09,39,39,39.73,40,40,0.984,0.01373 +VBS45724-6143STDY8787433,34.51,34,34,34.28,34,34,34.63,34,34,34.74,35,34,34.46,34,34,34.51,34,34,0.984,0.01378 +VBS45728-6143STDY8787434,49.49,49,49,49.16,49,49,49.6,49,49,49.69,50,50,49.47,50,50,49.73,50,49,0.984,0.0138 +VBS45734-6143STDY8787435,33.45,33,33,33.27,33,33,33.67,33,33,33.43,33,33,33.65,33,33,33.23,33,33,0.984,0.01379 +VBS45735-6143STDY8787436,33.51,33,33,33.25,33,33,33.58,33,33,33.75,34,33,33.47,33,33,33.7,34,33,0.984,0.01378 +VBS45737-6143STDY8787437,38.95,39,39,38.77,39,38,39.12,39,39,39.23,39,39,38.87,39,39,38.77,39,38,0.984,0.01379 +VBS45738-6143STDY8787438,39.63,40,39,39.44,39,39,39.84,40,39,39.87,40,39,39.46,39,39,39.57,39,39,0.984,0.01378 +VBS45739-6143STDY8787439,38.75,39,38,38.43,38,38,39.04,39,39,38.71,39,38,39.04,39,39,38.59,38,38,0.984,0.01376 +VBS45742-6143STDY8787440,43.47,43,43,43.37,43,44,43.52,43,43,43.55,43,43,43.32,43,43,43.61,43,43,0.984,0.01376 +VBS45743-6143STDY8787441,41.01,41,41,41.0,41,41,41.3,41,41,41.51,41,41,40.23,40,40,40.81,41,41,0.984,0.01376 VBS45745-6143STDY8787442,46.48,46,46,46.58,46,46,46.9,46,46,47.01,47,46,45.45,45,45,46.04,46,46,0.984,0.01381 diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv index 5beda0a88..4dc0578d7 100644 --- a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00151/wgs_accession_data.csv @@ -1,27 +1,27 @@ -sample_id,run_ena -VBS45687-6143STDY8787412,"ERR4696346, ERR4766075, ERR4766106" -VBS45688-6143STDY8787413,"ERR4696347, ERR4766076, ERR4766107" -VBS45689-6143STDY8787414,"ERR4696348, ERR4766077, ERR4766108" -VBS45690-6143STDY8787415,"ERR4696349, ERR4766078, ERR4766109" -VBS45691-6143STDY8787416,"ERR4696350, ERR4766079, ERR4766110" -VBS45692-6143STDY8787417,"ERR4696351, ERR4766080, ERR4766111" -VBS45701-6143STDY8787420,"ERR4696354, ERR4766083, ERR4766114" -VBS45702-6143STDY8787421,"ERR4696355, ERR4766084, ERR4766115" -VBS45708-6143STDY8787424,"ERR4696358, ERR4766087, ERR4766118" -VBS45709-6143STDY8787425,"ERR4696359, ERR4766088, ERR4766119" -VBS45711-6143STDY8787426,"ERR4696360, ERR4766089, ERR4766120" -VBS45713-6143STDY8787427,"ERR4696361, ERR4766090, ERR4766121" -VBS45717-6143STDY8787429,"ERR4696363, ERR4766092, ERR4766123" -VBS45718-6143STDY8787430,"ERR4696364, ERR4766093, ERR4766124" -VBS45720-6143STDY8787431,"ERR4696365, ERR4766094, ERR4766125" -VBS45723-6143STDY8787432,"ERR4696366, ERR4766095, ERR4766126" -VBS45724-6143STDY8787433,"ERR4696367, ERR4766096, ERR4766127" -VBS45728-6143STDY8787434,"ERR4696368, ERR4766097, ERR4766128" -VBS45734-6143STDY8787435,"ERR4696369, ERR4766098, ERR4766129" -VBS45735-6143STDY8787436,"ERR4696370, ERR4766099, ERR4766130" -VBS45737-6143STDY8787437,"ERR4696371, ERR4766100, ERR4766131" -VBS45738-6143STDY8787438,"ERR4696372, ERR4766101, ERR4766132" -VBS45739-6143STDY8787439,"ERR4696373, ERR4766102, ERR4766133" -VBS45742-6143STDY8787440,"ERR4696374, ERR4766103, ERR4766134" -VBS45743-6143STDY8787441,"ERR4696375, ERR4766104, ERR4766135" -VBS45745-6143STDY8787442,"ERR4696376, ERR4766105, ERR4766136" +sample_id,run_ena,analysis_ena +VBS45687-6143STDY8787412,, +VBS45688-6143STDY8787413,, +VBS45689-6143STDY8787414,, +VBS45690-6143STDY8787415,, +VBS45691-6143STDY8787416,, +VBS45692-6143STDY8787417,, +VBS45701-6143STDY8787420,, +VBS45702-6143STDY8787421,, +VBS45708-6143STDY8787424,, +VBS45709-6143STDY8787425,, +VBS45711-6143STDY8787426,, +VBS45713-6143STDY8787427,, +VBS45717-6143STDY8787429,, +VBS45718-6143STDY8787430,, +VBS45720-6143STDY8787431,, +VBS45723-6143STDY8787432,, +VBS45724-6143STDY8787433,, +VBS45728-6143STDY8787434,, +VBS45734-6143STDY8787435,, +VBS45735-6143STDY8787436,, +VBS45737-6143STDY8787437,, +VBS45738-6143STDY8787438,, +VBS45739-6143STDY8787439,, +VBS45742-6143STDY8787440,, +VBS45743-6143STDY8787441,, +VBS45745-6143STDY8787442,, diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/samples.meta.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/samples.meta.csv new file mode 100644 index 000000000..2e34e6332 --- /dev/null +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1277-VO-KH-WITKOWSKI-VMF00183/samples.meta.csv @@ -0,0 +1,249 @@ +sample_id,partner_sample_id,contributor,country,location,year,month,latitude,longitude,sex_call +VBS54551-6143STDY11462443,BC1861,Amelie Vantaux,Cambodia,FOH05,2019,10,12.285,106.994,UKN +VBS54553-6143STDY11462445,BC1867,Amelie Vantaux,Cambodia,FOH05,2019,10,12.285,106.994,UKN +VBS54554-6143STDY11462446,BC1876,Amelie Vantaux,Cambodia,FOH05,2019,10,12.285,106.994,UKN +VBS54555-6143STDY11462447,BC1877,Amelie Vantaux,Cambodia,FOH05,2019,10,12.285,106.994,UKN +VBS54556-6143STDY11462448,BC1881,Amelie Vantaux,Cambodia,FOH05,2019,10,12.285,106.994,UKN +VBS54557-6143STDY11462449,BC1883,Amelie Vantaux,Cambodia,FOH05,2019,10,12.285,106.994,UKN +VBS54558-6143STDY11462450,BC1890,Amelie Vantaux,Cambodia,FOH05,2019,10,12.285,106.994,UKN +VBS54561-6143STDY11462453,BC1895,Amelie Vantaux,Cambodia,FOH05,2019,10,12.285,106.994,UKN 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a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/samples.meta.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/samples.meta.csv new file mode 100644 index 000000000..ece09c8b3 --- /dev/null +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/samples.meta.csv @@ -0,0 +1,220 @@ +sample_id,partner_sample_id,contributor,country,location,year,month,latitude,longitude,sex_call +VBS45974-6296STDY9478582,329,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, A",2019,2,9.110,98.878,UKN +VBS45976-6296STDY9478584,339,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, A/2",2019,2,9.110,98.878,UKN +VBS45979-6296STDY9478587,920,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, C2",2019,3,9.134,98.888,UKN +VBS45982-6296STDY9478589,1007,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, C2",2019,4,9.134,98.888,UKN +VBS46005-6296STDY9478612,1845,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46042-6296STDY9478649,2014,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46050-6296STDY9478657,2043,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46059-6296STDY9478666,2523,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,UKN +VBS46066-6296STDY9478673,2909,Kevin Kobylinski,Thailand,"Phanom, three, C1",2019,6,8.890,98.664,UKN +VBS46067-6296STDY9478674,2935,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,UKN +VBS46078-6296STDY9478687,3109,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46083-6296STDY9478692,3185,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,UKN +VBS46084-6296STDY9478693,3191,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,UKN +VBS46087-6296STDY9478696,3325,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,UKN +VBS46088-6296STDY9478697,3330,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,UKN +VBS46098-6296STDY9478707,3932_1278,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,3,9.340,98.880,UKN +VBS46121-6296STDY9478730,4591,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46141-6296STDY9478750,5202,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46145-6296STDY9478754,5206,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46146-6296STDY9478755,5209,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46154-6296STDY9478763,5221,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46168-6296STDY9478779,5244,Kevin Kobylinski,Thailand,"Vibhavadi, six, A",2019,10,9.252,98.850,UKN +VBS46172-6296STDY9478782,5265,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,10,9.340,98.880,UKN +VBS46173-6296STDY9478783,5313,Kevin Kobylinski,Thailand,"Vibhavadi, ten, F",2019,10,9.353,98.875,UKN +VBS46175-6296STDY9478785,5496,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46180-6296STDY9478790,5506_1278,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46183-6296STDY9478793,5592,Kevin Kobylinski,Thailand,"Vibhavadi, eight, I",2019,10,9.296,98.886,UKN +VBS46187-6296STDY9478797,5614,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,UKN +VBS46188-6296STDY9478798,5619,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,UKN +VBS46189-6296STDY9478799,5647,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46190-6296STDY9478800,5649,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46192-6296STDY9478801,5683,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, N",2019,10,9.083,98.878,UKN +VBS46198-6296STDY9478807,5736,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS45975-6296STDY10244530,331,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, A",2019,2,9.110,98.878,UKN +VBS45983-6296STDY10244537,1200,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, C1",2019,4,9.080,98.879,UKN +VBS45984-6296STDY10244538,1363,Kevin Kobylinski,Thailand,"Phanom, three, A2",2019,4,8.894,98.667,UKN +VBS45985-6296STDY10244539,1364,Kevin Kobylinski,Thailand,"Phanom, three, A2",2019,4,8.894,98.667,UKN +VBS45986-6296STDY10244540,1494,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, D1",2019,4,9.107,98.869,UKN +VBS45987-6296STDY10244541,1498,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, D2",2019,4,9.107,98.869,UKN +VBS45988-6296STDY10244542,1687,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45989-6296STDY10244543,1688,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45991-6296STDY10244545,1711,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS45992-6296STDY10244546,1719,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45993-6296STDY10244547,1738,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45994-6296STDY10244548,1750,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45995-6296STDY10244549,1759,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45996-6296STDY10244550,1771,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45997-6296STDY10244551,1774,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS45998-6296STDY10244552,1780,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS45999-6296STDY10244553,1793,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46000-6296STDY10244554,1810,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46001-6296STDY10244555,1818,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46002-6296STDY10244556,1826_1278,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46003-6296STDY10244557,1830,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46004-6296STDY10244558,1840,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46006-6296STDY10244560,1854,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46007-6296STDY10244561,1859,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46008-6296STDY10244562,1860,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46009-6296STDY10244563,1866,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46010-6296STDY10244564,1871,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46011-6296STDY10244565,1872,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46012-6296STDY10244566,1875,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46013-6296STDY10244567,1881,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46014-6296STDY10244568,1887,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46016-6296STDY10244570,1908,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46017-6296STDY10244571,1912,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46019-6296STDY10244573,1931,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46020-6296STDY10244574,1932,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46021-6296STDY10244575,1934,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46022-6296STDY10244576,1936,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46025-6296STDY10244579,1946,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46026-6296STDY10244580,1949,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46027-6296STDY10244581,1950,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46028-6296STDY10244582,1951,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46029-6296STDY10244583,1954,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46030-6296STDY10244584,1956,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46031-6296STDY10244585,1960,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46032-6296STDY10244586,1966,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46033-6296STDY10244587,1975,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46034-6296STDY10244588,1977,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46035-6296STDY10244589,1978,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46036-6296STDY10244590,1989,Kevin Kobylinski,Thailand,"Phanom, one, B1",2019,5,8.870,98.631,UKN +VBS46037-6296STDY10244591,1999,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46038-6296STDY10244592,2000,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46039-6296STDY10244593,2003,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46040-6296STDY10244594,2006,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46041-6296STDY10244595,2011,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46043-6296STDY10244597,2017,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46044-6296STDY10244598,2018,Kevin Kobylinski,Thailand,"Phanom, one, B2",2019,5,8.869,98.631,UKN +VBS46045-6296STDY10244599,2028,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46046-6296STDY10244600,2037,Kevin Kobylinski,Thailand,"Phanom, three, B2",2019,5,8.896,98.663,UKN +VBS46047-6296STDY10244601,2039,Kevin Kobylinski,Thailand,"Phanom, three, B2",2019,5,8.896,98.663,UKN +VBS46048-6296STDY10244602,2040,Kevin Kobylinski,Thailand,"Phanom, three, B2",2019,5,8.896,98.663,UKN +VBS46049-6296STDY10244603,2041,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46051-6296STDY10244605,2044,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46052-6296STDY10244606,2045,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46053-6296STDY10244607,2047,Kevin Kobylinski,Thailand,"Phanom, three, B1",2019,5,8.896,98.663,UKN +VBS46054-6296STDY10244608,2431,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E1",2019,5,9.068,98.846,UKN +VBS46055-6296STDY10244609,2444,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,UKN +VBS46056-6296STDY10244610,2499,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,UKN +VBS46057-6296STDY10244611,2503,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, E2",2019,5,9.068,98.846,UKN +VBS46060-6296STDY10244614,2569,Kevin Kobylinski,Thailand,"Vibhavadi, eleven, A",2019,5,9.360,98.876,UKN +VBS46061-6296STDY10244615,2688,Kevin Kobylinski,Thailand,"Vibhavadi, nine, A3",2019,1,9.331,98.878,UKN +VBS46063-6296STDY10244617,2841,Kevin Kobylinski,Thailand,"Phanom, three, C2",2019,6,8.890,98.663,UKN +VBS46064-6296STDY10244618,2889,Kevin Kobylinski,Thailand,"Phanom, three, C1",2019,6,8.890,98.664,UKN +VBS46065-6296STDY10244619,2894,Kevin Kobylinski,Thailand,"Phanom, three, C1",2019,6,8.890,98.664,UKN +VBS46068-6296STDY10244622,2937,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,UKN +VBS46069-6296STDY10244625,2944,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46070-6296STDY10244626,2960,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46071-6296STDY10244627,2961,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46072-6296STDY10244628,3007,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46073-6296STDY10244629,3037,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, H",2019,6,9.136,98.881,UKN +VBS46074-6296STDY10244630,3041,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, H",2019,6,9.136,98.881,UKN +VBS46075-6296STDY10244631,3062,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, F",2019,6,9.105,98.891,UKN +VBS46076-6296STDY10244632,3077,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,UKN +VBS46077-6296STDY10244633,3079,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, G",2019,6,9.108,98.885,UKN +VBS46079-6296STDY10244635,3129,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, G",2019,6,9.135,98.882,UKN +VBS46080-6296STDY10244636,3142,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, G",2019,6,9.063,98.877,UKN +VBS46081-6296STDY10244637,3170,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,UKN +VBS46082-6296STDY10244638,3183,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,UKN +VBS46085-6296STDY10244641,3249,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,6,9.082,98.861,UKN +VBS46086-6296STDY10244642,3316,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, F",2019,6,9.081,98.864,UKN +VBS46089-6296STDY10244645,3388,Kevin Kobylinski,Thailand,"Vibhavadi, eight, B1",2019,7,9.304,98.885,UKN +VBS46090-6296STDY10244646,3396,Kevin Kobylinski,Thailand,"Vibhavadi, eight, B1",2019,7,9.304,98.885,UKN +VBS46091-6296STDY10244647,3397,Kevin Kobylinski,Thailand,"Vibhavadi, eight, B2",2019,7,9.304,98.886,UKN +VBS46092-6296STDY10244648,3581,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, H",2019,7,9.110,98.880,UKN +VBS46093-6296STDY10244649,3623,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, I",2019,7,9.052,98.865,UKN +VBS46094-6296STDY10244650,3710,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, I",2019,7,9.140,98.881,UKN +VBS46095-6296STDY10244651,3745,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, I",2019,7,9.052,98.865,UKN +VBS46096-6296STDY10244652,3780,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, G",2019,7,9.082,98.861,UKN +VBS46097-6296STDY10244653,3840,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,3,9.340,98.880,UKN +VBS46099-6296STDY10244655,3954,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,3,9.340,98.880,UKN +VBS46100-6296STDY10244656,4148,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, J",2019,8,9.111,98.881,UKN +VBS46101-6296STDY10244657,4149,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, J",2019,8,9.111,98.881,UKN +VBS46102-6296STDY10244658,4151,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, J",2019,8,9.111,98.881,UKN +VBS46103-6296STDY10244659,4156_1278,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, I",2019,8,9.105,98.889,UKN +VBS46104-6296STDY10244660,4235,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, M",2019,8,9.126,98.903,UKN +VBS46105-6296STDY10244661,4274,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, I",2019,8,9.105,98.889,UKN +VBS46106-6296STDY10244662,4310,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46107-6296STDY10244663,4321,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46108-6296STDY10244664,4407,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, K",2019,8,9.084,98.876,UKN +VBS46109-6296STDY10244665,4430,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, K",2019,8,9.084,98.876,UKN +VBS46110-6296STDY10244666,4472,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, J",2019,8,9.053,98.852,UKN +VBS46111-6296STDY10244667,4488,Kevin Kobylinski,Thailand,"Khirirat Nikhom, four, K",2019,8,9.052,98.857,UKN +VBS46112-6296STDY10244668,4511,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, K",2019,8,9.084,98.876,UKN +VBS46113-6296STDY10244669,4556,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46114-6296STDY10244670,4560,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46115-6296STDY10244671,4577,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46116-6296STDY10244672,4578,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46117-6296STDY10244673,4579,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46118-6296STDY10244674,4585,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, A",2019,8,9.100,98.896,UKN +VBS46119-6296STDY10244675,4589,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46120-6296STDY10244676,4590,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46122-6296STDY10244678,4596,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46123-6296STDY10244679,4609,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, B",2019,8,9.099,98.898,UKN +VBS46124-6296STDY10244680,4666,Kevin Kobylinski,Thailand,"Vibhavadi, eight, F",2019,2,9.307,98.885,UKN +VBS46125-6296STDY10244681,4768,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46126-6296STDY10244682,4778,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46127-6296STDY10244683,4779,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46128-6296STDY10244684,4788,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46129-6296STDY10244685,4809,Kevin Kobylinski,Thailand,"Vibhavadi, nine, B",2019,2,9.326,98.876,UKN +VBS46130-6296STDY10244686,4875,Kevin Kobylinski,Thailand,"Vibhavadi, ten, D",2019,2,9.340,98.880,UKN +VBS46131-6296STDY10244687,5191_1278,Kevin Kobylinski,Thailand,"Phanom, one, F",2019,10,8.869,98.638,UKN +VBS46132-6296STDY10244688,5192,Kevin Kobylinski,Thailand,"Phanom, one, F",2019,10,8.869,98.638,UKN +VBS46133-6296STDY10244689,5194,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46134-6296STDY10244690,5195,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46135-6296STDY10244691,5196,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46136-6296STDY10244692,5197,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46137-6296STDY10244693,5198,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46138-6296STDY10244694,5199,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46139-6296STDY10244695,5200,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46140-6296STDY10244696,5201,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46142-6296STDY10244698,5203,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46143-6296STDY10244699,5204,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46144-6296STDY10244700,5205,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46147-6296STDY10244703,5214,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46148-6296STDY10244704,5215,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46149-6296STDY10244705,5216,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46150-6296STDY10244706,5217,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46151-6296STDY10244707,5218,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46152-6296STDY10244708,5219,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46153-6296STDY10244709,5220,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46155-6296STDY10244711,5222,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46156-6296STDY10244712,5223,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46157-6296STDY10244713,5226,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46158-6296STDY10244714,5227,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46160-6296STDY10244716,5230_1278,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46161-6296STDY10244717,5231,Kevin Kobylinski,Thailand,"Phanom, one, G",2019,10,8.877,98.646,UKN +VBS46162-6296STDY10244718,5232,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46163-6296STDY10244721,5233,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46164-6296STDY10244722,5236,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46165-6296STDY10244723,5237,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46166-6296STDY10244724,5238,Kevin Kobylinski,Thailand,"Phanom, one, E",2019,10,8.871,98.641,UKN +VBS46170-6296STDY10244727,5247,Kevin Kobylinski,Thailand,"Vibhavadi, nine, D",2019,10,9.327,98.877,UKN +VBS46171-6296STDY10244728,5248,Kevin Kobylinski,Thailand,"Vibhavadi, nine, D",2019,10,9.327,98.877,UKN +VBS46174-6296STDY10244731,5494,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46176-6296STDY10244733,5500,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46177-6296STDY10244734,5501,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46178-6296STDY10244735,5502,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46179-6296STDY10244736,5505,Kevin Kobylinski,Thailand,"Vibhavadi, nine, E",2019,10,9.329,98.873,UKN +VBS46181-6296STDY10244738,5542,Kevin Kobylinski,Thailand,"Vibhavadi, eight, I",2019,10,9.296,98.886,UKN +VBS46182-6296STDY10244739,5548,Kevin Kobylinski,Thailand,"Vibhavadi, eight, I",2019,10,9.296,98.886,UKN +VBS46184-6296STDY10244741,5604,Kevin Kobylinski,Thailand,"Khirirat Nikhom, five, B",2019,10,9.043,98.894,UKN +VBS46185-6296STDY10244742,5609,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,UKN +VBS46186-6296STDY10244743,5613,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, L",2019,10,9.083,98.859,UKN +VBS46193-6296STDY10244749,5697,Kevin Kobylinski,Thailand,"Khirirat Nikhom, six, O",2019,10,9.076,98.868,UKN +VBS46194-6296STDY10244750,5721,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46195-6296STDY10244751,5725,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46196-6296STDY10244752,5727,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46197-6296STDY10244753,5728,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46199-6296STDY10244755,5738,Kevin Kobylinski,Thailand,"Khirirat Nikhom, seven, D",2019,10,9.097,98.902,UKN +VBS46200-6296STDY10244756,5765,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, K",2019,10,9.108,98.875,UKN +VBS46201-6296STDY10244757,5771,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, K",2019,10,9.108,98.875,UKN +VBS46202-6296STDY10244758,5777,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, L",2019,10,9.109,98.877,UKN +VBS46203-6296STDY10244759,5895,Kevin Kobylinski,Thailand,"Khirirat Nikhom, nine, Q",2019,10,9.127,98.905,UKN +VBS46204-6296STDY10244760,5972,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, M",2019,10,9.104,98.891,UKN +VBS46205-6296STDY10244761,6024,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, M",2019,10,9.104,98.891,UKN +VBS46206-6296STDY10244762,6036,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, N",2019,10,9.106,98.887,UKN +VBS46207-6296STDY10244763,6037,Kevin Kobylinski,Thailand,"Khirirat Nikhom, eight, N",2019,10,9.106,98.887,UKN diff --git a/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv new file mode 100644 index 000000000..41e1c652b --- /dev/null +++ b/tests/anoph/fixture/vo_adir_release_master_us_central1/v1.0/metadata/general/1278-VO-TH-KOBYLINSKI-VMF00153/sequence_qc_stats.csv @@ -0,0 +1,220 @@ +sample_id,mean_cov,median_cov,modal_cov,mean_cov_KB672490,median_cov_KB672490,mode_cov_KB672490,mean_cov_KB672868,median_cov_KB672868,mode_cov_KB672868,mean_cov_KB672979,median_cov_KB672979,mode_cov_KB672979,mean_cov_KB673090,median_cov_KB673090,mode_cov_KB673090,mean_cov_KB673201,median_cov_KB673201,mode_cov_KB673201,frac_gen_cov,divergence +VBS45974-6296STDY9478582,9.79,9,9,9.79,9,9,9.81,9,9,9.91,10,9,9.81,9,9,9.62,9,9,0.952,0.03652 +VBS45975-6296STDY10244530,75.33,76,75,74.27,74,75,74.89,75,75,76.6,76,75,76.95,78,77,74.97,75,75,0.959,0.03382 +VBS45976-6296STDY9478584,12.9,13,12,12.95,13,12,12.87,13,12,13.16,13,12,12.6,12,12,12.83,13,12,0.952,0.03517 +VBS45979-6296STDY9478587,14.53,14,14,14.56,14,14,14.39,14,14,14.72,14,14,14.56,14,14,14.42,14,14,0.954,0.03525 +VBS45982-6296STDY9478589,20.34,19,18,20.91,20,19,20.46,19,18,20.86,20,18,19.02,18,17,19.81,19,18,0.955,0.03414 +VBS45983-6296STDY10244537,16.39,16,16,16.38,16,16,16.34,16,16,16.93,17,16,16.07,16,16,16.19,16,16,0.955,0.03482 +VBS45984-6296STDY10244538,36.46,37,37,36.39,36,36,36.38,36,37,37.05,37,37,36.14,36,37,36.36,36,37,0.957,0.03366 +VBS45985-6296STDY10244539,37.61,38,38,37.81,38,38,37.37,37,38,38.91,39,38,36.55,37,36,37.22,37,37,0.957,0.03361 +VBS45986-6296STDY10244540,42.12,42,42,42.54,43,42,42.04,42,42,43.8,44,43,40.26,41,41,41.4,42,41,0.956,0.03393 +VBS45987-6296STDY10244541,37.26,37,37,37.56,37,37,37.37,37,37,38.76,39,38,35.6,36,36,36.47,37,36,0.957,0.03383 +VBS45988-6296STDY10244542,38.39,39,39,38.55,39,39,38.36,38,39,39.36,39,39,37.31,38,38,38.11,38,39,0.958,0.03386 +VBS45989-6296STDY10244543,49.81,50,50,49.82,50,50,49.57,50,50,51.36,51,51,48.79,49,49,49.44,50,50,0.957,0.03365 +VBS45991-6296STDY10244545,45.77,46,46,46.01,46,47,45.76,46,46,47.23,47,47,44.29,45,46,45.2,46,46,0.958,0.03387 +VBS45992-6296STDY10244546,37.63,38,38,37.58,38,37,37.6,38,38,38.71,39,38,36.73,37,37,37.43,37,37,0.957,0.03359 +VBS45993-6296STDY10244547,38.07,38,38,38.01,38,38,37.95,38,38,39.0,39,39,37.58,38,38,37.81,38,38,0.957,0.03362 +VBS45994-6296STDY10244548,44.41,45,45,44.32,44,44,44.24,44,44,45.33,45,45,43.8,44,45,44.44,45,45,0.957,0.03363 +VBS45995-6296STDY10244549,38.14,38,38,37.9,38,38,38.13,38,39,39.34,39,39,37.46,38,38,37.94,38,38,0.955,0.03396 +VBS45996-6296STDY10244550,36.73,37,37,36.41,36,36,36.66,37,36,37.77,38,37,36.51,37,37,36.47,37,37,0.957,0.0336 +VBS45997-6296STDY10244551,76.86,78,79,77.22,78,79,76.63,78,79,79.64,80,81,74.05,76,77,76.28,77,78,0.959,0.03383 +VBS45998-6296STDY10244552,64.83,65,66,65.01,65,65,65.03,65,65,66.89,67,67,62.63,64,65,64.1,65,65,0.959,0.03395 +VBS45999-6296STDY10244553,45.76,46,46,45.75,46,46,45.62,46,46,48.71,49,49,43.74,44,45,44.72,45,45,0.958,0.03387 +VBS46000-6296STDY10244554,89.13,90,91,89.65,91,92,88.16,90,90,93.33,94,93,85.9,88,90,88.3,90,89,0.959,0.03382 +VBS46001-6296STDY10244555,35.07,35,35,34.88,35,35,35.04,35,35,36.13,36,36,34.34,34,35,35.01,35,35,0.957,0.03358 +VBS46002-6296STDY10244556,40.42,40,39,40.36,40,38,40.37,40,39,41.57,41,40,39.71,39,38,40.07,39,39,0.957,0.03366 +VBS46003-6296STDY10244557,42.55,42,41,42.5,42,41,42.5,42,41,44.01,44,42,41.62,41,40,41.99,42,41,0.957,0.03363 +VBS46004-6296STDY10244558,42.06,42,42,42.35,42,42,42.17,42,42,44.16,44,44,39.92,40,41,41.1,41,41,0.958,0.03388 +VBS46005-6296STDY9478612,18.82,18,18,18.97,19,18,18.76,18,18,19.12,19,18,18.45,18,17,18.67,18,18,0.955,0.0338 +VBS46006-6296STDY10244560,43.63,44,44,43.5,44,43,43.55,44,44,45.64,46,45,42.36,43,43,43.05,43,43,0.957,0.03363 +VBS46007-6296STDY10244561,39.77,40,40,39.87,40,40,39.84,40,40,40.96,41,40,38.65,39,40,39.24,40,40,0.958,0.03385 +VBS46008-6296STDY10244562,39.04,39,39,39.03,39,39,38.83,39,38,40.34,40,40,38.26,38,39,38.76,39,39,0.957,0.03369 +VBS46009-6296STDY10244563,34.34,34,34,34.29,34,34,34.16,34,34,35.53,35,35,33.61,34,34,34.17,34,34,0.957,0.03363 +VBS46010-6296STDY10244564,44.3,44,44,44.3,44,44,44.4,44,44,45.98,46,45,42.63,43,43,43.95,44,44,0.957,0.03363 +VBS46011-6296STDY10244565,37.81,38,38,37.88,38,38,37.62,38,37,39.19,39,39,36.74,37,37,37.47,37,37,0.958,0.03362 +VBS46012-6296STDY10244566,49.18,49,50,49.36,50,49,49.33,50,50,51.23,51,52,47.19,48,49,48.3,49,49,0.958,0.03389 +VBS46013-6296STDY10244567,49.91,50,51,50.07,50,50,49.97,50,50,51.84,52,52,47.97,49,50,49.29,50,50,0.959,0.03389 +VBS46014-6296STDY10244568,68.98,70,70,68.7,69,70,68.88,69,70,72.02,72,72,67.07,68,69,68.18,69,69,0.958,0.03375 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b/tests/anoph/test_g123.py index 6ab324d1d..ea03462dc 100644 --- a/tests/anoph/test_g123.py +++ b/tests/anoph/test_g123.py @@ -72,7 +72,7 @@ def adir1_sim_api(adir1_sim_fixture): default_site_mask="dirus", results_cache=adir1_sim_fixture.results_cache_path.as_posix(), taxon_colors=_adir1.TAXON_COLORS, - default_phasing_analysis="dirus_noneyet", + default_phasing_analysis="all", ) From 4989f74f6ab883046ae4dec25b3e83420e3d59fb Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 25 Nov 2025 11:26:18 +1000 Subject: [PATCH 36/41] remove tests for g123 and dipclust --- tests/anoph/test_dipclust.py | 19 ------------------- tests/anoph/test_fst.py | 19 ------------------- 2 files changed, 38 deletions(-) diff --git a/tests/anoph/test_dipclust.py b/tests/anoph/test_dipclust.py index 72e003b94..591d39511 100644 --- a/tests/anoph/test_dipclust.py +++ b/tests/anoph/test_dipclust.py @@ -4,7 +4,6 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 -from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.dipclust import AnophelesDipClustAnalysis @@ -61,24 +60,6 @@ def af1_sim_api(af1_sim_fixture): ) -@pytest.fixture -def adir1_sim_api(adir1_sim_fixture): - return AnophelesDipClustAnalysis( - url=adir1_sim_fixture.url, - public_url=adir1_sim_fixture.url, - config_path=_adir1.CONFIG_PATH, - major_version_number=_adir1.MAJOR_VERSION_NUMBER, - major_version_path=_adir1.MAJOR_VERSION_PATH, - pre=False, - gff_gene_type="protein_coding_gene", - gff_gene_name_attribute="Note", - gff_default_attributes=("ID", "Parent", "Note", "description"), - default_site_mask="dirus", - results_cache=adir1_sim_fixture.results_cache_path.as_posix(), - taxon_colors=_adir1.TAXON_COLORS, - ) - - # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for diff --git a/tests/anoph/test_fst.py b/tests/anoph/test_fst.py index 8cfaea808..ba9dfa4a0 100644 --- a/tests/anoph/test_fst.py +++ b/tests/anoph/test_fst.py @@ -9,7 +9,6 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 -from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.fst import AnophelesFstAnalysis @@ -58,24 +57,6 @@ def af1_sim_api(af1_sim_fixture): ) -@pytest.fixture -def adir1_sim_api(adir1_sim_fixture): - return AnophelesFstAnalysis( - url=adir1_sim_fixture.url, - public_url=adir1_sim_fixture.url, - config_path=_adir1.CONFIG_PATH, - major_version_number=_adir1.MAJOR_VERSION_NUMBER, - major_version_path=_adir1.MAJOR_VERSION_PATH, - pre=False, - gff_gene_type="protein_coding_gene", - gff_gene_name_attribute="Note", - gff_default_attributes=("ID", "Parent", "Note", "description"), - default_site_mask="dirus", - results_cache=adir1_sim_fixture.results_cache_path.as_posix(), - taxon_colors=_adir1.TAXON_COLORS, - ) - - # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for From ac9677e2c47a94acc4b8a122d7176b25b5105413 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 25 Nov 2025 13:53:32 +1000 Subject: [PATCH 37/41] more test fixes --- tests/anoph/test_dipclust.py | 4 ---- tests/anoph/test_fst.py | 19 +++++++++++++++++++ tests/anoph/test_g123.py | 24 ------------------------ 3 files changed, 19 insertions(+), 28 deletions(-) diff --git a/tests/anoph/test_dipclust.py b/tests/anoph/test_dipclust.py index 591d39511..c0bbad033 100644 --- a/tests/anoph/test_dipclust.py +++ b/tests/anoph/test_dipclust.py @@ -80,10 +80,6 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api -def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): - return adir1_sim_fixture, adir1_sim_api - - @pytest.mark.parametrize("distance_metric", ["cityblock", "euclidean"]) @parametrize_with_cases("fixture,api", cases=".") def test_plot_diplotype_clustering( diff --git a/tests/anoph/test_fst.py b/tests/anoph/test_fst.py index ba9dfa4a0..8cfaea808 100644 --- a/tests/anoph/test_fst.py +++ b/tests/anoph/test_fst.py @@ -9,6 +9,7 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 +from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.fst import AnophelesFstAnalysis @@ -57,6 +58,24 @@ def af1_sim_api(af1_sim_fixture): ) +@pytest.fixture +def adir1_sim_api(adir1_sim_fixture): + return AnophelesFstAnalysis( + url=adir1_sim_fixture.url, + public_url=adir1_sim_fixture.url, + config_path=_adir1.CONFIG_PATH, + major_version_number=_adir1.MAJOR_VERSION_NUMBER, + major_version_path=_adir1.MAJOR_VERSION_PATH, + pre=False, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + default_site_mask="dirus", + results_cache=adir1_sim_fixture.results_cache_path.as_posix(), + taxon_colors=_adir1.TAXON_COLORS, + ) + + # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for diff --git a/tests/anoph/test_g123.py b/tests/anoph/test_g123.py index ea03462dc..ab5e25537 100644 --- a/tests/anoph/test_g123.py +++ b/tests/anoph/test_g123.py @@ -6,7 +6,6 @@ from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 -from malariagen_data import adir1 as _adir1 from malariagen_data.anoph.g123 import AnophelesG123Analysis @@ -57,25 +56,6 @@ def af1_sim_api(af1_sim_fixture): ) -@pytest.fixture -def adir1_sim_api(adir1_sim_fixture): - return AnophelesG123Analysis( - url=adir1_sim_fixture.url, - public_url=adir1_sim_fixture.url, - config_path=_adir1.CONFIG_PATH, - major_version_number=_adir1.MAJOR_VERSION_NUMBER, - major_version_path=_adir1.MAJOR_VERSION_PATH, - pre=False, - gff_gene_type="protein_coding_gene", - gff_gene_name_attribute="Note", - gff_default_attributes=("ID", "Parent", "Note", "description"), - default_site_mask="dirus", - results_cache=adir1_sim_fixture.results_cache_path.as_posix(), - taxon_colors=_adir1.TAXON_COLORS, - default_phasing_analysis="all", - ) - - # N.B., here we use pytest_cases to parametrize tests. Each # function whose name begins with "case_" defines a set of # inputs to the test functions. See the documentation for @@ -96,10 +76,6 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api -def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): - return adir1_sim_fixture, adir1_sim_api - - def check_g123_gwss(*, api, g123_params): # Run main gwss function under test. x, g123 = api.g123_gwss(**g123_params) From 5956494b4a46c3fce53491d73828e671c8be5faf Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Wed, 26 Nov 2025 08:49:08 +1000 Subject: [PATCH 38/41] add surveillance/restricted use flags --- malariagen_data/adir1.py | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index 5b2f28799..ff6db0679 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -86,6 +86,8 @@ def __init__( discordant_read_calls_analysis=None, pre=False, tqdm_class=None, + unrestricted_use_only=False, + surveillance_use_only=False, **storage_options, # used by fsspec via init_filesystem() ): super().__init__( @@ -122,6 +124,8 @@ def __init__( virtual_contigs=None, gene_names=None, inversion_tag_path=None, + unrestricted_use_only=unrestricted_use_only, + surveillance_use_only=surveillance_use_only, ) def __repr__(self): @@ -199,6 +203,24 @@ def _repr_html_(self): {self.client_location} + + + Data filtered for unrestricted use only + + {self._unrestricted_use_only} + + + + Data filtered for surveillance use only + + {self._surveillance_use_only} + + + + Relevant data releases + + {', '.join(self.releases)} + """ From 826a920c11d64f5ab9e3922598fba6bc158161bf Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Wed, 26 Nov 2025 08:50:49 +1000 Subject: [PATCH 39/41] add surveillance/restricted use flags again --- malariagen_data/adir1.py | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index ff6db0679..301c38b3f 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -131,13 +131,16 @@ def __init__( def __repr__(self): text = ( f"\n" - f"Storage URL : {self._url}\n" - f"Data releases available : {', '.join(self.releases)}\n" - f"Results cache : {self._results_cache}\n" - f"Cohorts analysis : {self._cohorts_analysis}\n" - f"Site filters analysis : {self._site_filters_analysis}\n" - f"Software version : malariagen_data {malariagen_data.__version__}\n" - f"Client location : {self.client_location}\n" + f"Storage URL : {self._url}\n" + f"Data releases available : {', '.join(self._available_releases)}\n" + f"Results cache : {self._results_cache}\n" + f"Cohorts analysis : {self._cohorts_analysis}\n" + f"Site filters analysis : {self._site_filters_analysis}\n" + f"Software version : malariagen_data {malariagen_data.__version__}\n" + f"Client location : {self.client_location}\n" + f"Data filtered to unrestricted use only: {self._unrestricted_use_only}\n" + f"Data filtered to surveillance use only: {self._surveillance_use_only}\n" + f"Relevant data releases : {', '.join(self.releases)}\n" f"---\n" f"Please note that data are subject to terms of use,\n" f"for more information see https://www.malariagen.net/data\n" @@ -171,7 +174,7 @@ def _repr_html_(self): Data releases available - {', '.join(self.releases)} + {', '.join(self._available_releases)} From bebd52484876b543b3899113f7f1bd536bfc5f01 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Wed, 26 Nov 2025 09:02:00 +1000 Subject: [PATCH 40/41] Apply pre-commit formatting fixes --- tests/anoph/test_sample_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/anoph/test_sample_metadata.py b/tests/anoph/test_sample_metadata.py index 464e1cf3a..3120c8adb 100644 --- a/tests/anoph/test_sample_metadata.py +++ b/tests/anoph/test_sample_metadata.py @@ -164,7 +164,7 @@ def case_ag3_sim(ag3_sim_fixture, ag3_sim_api): @case def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api - + @case def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): From 5e358c254e1509588a540a0035c4266959aede6e Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Wed, 26 Nov 2025 12:50:26 +1000 Subject: [PATCH 41/41] skip tests for adir1 that have sex call query --- tests/anoph/test_snp_data.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/tests/anoph/test_snp_data.py b/tests/anoph/test_snp_data.py index 453a6ccef..d9cef5c23 100644 --- a/tests/anoph/test_snp_data.py +++ b/tests/anoph/test_snp_data.py @@ -9,7 +9,9 @@ import xarray as xr import zarr # type: ignore from numpy.testing import assert_array_equal -from pytest_cases import parametrize_with_cases +from pytest_cases import parametrize_with_cases, case +from pytest_cases import filters as ft + from malariagen_data import af1 as _af1 from malariagen_data import ag3 as _ag3 @@ -91,14 +93,17 @@ def adir1_sim_api(adir1_sim_fixture): # pytest alone. +@case(tags="ag3") def case_ag3_sim(ag3_sim_fixture, ag3_sim_api): return ag3_sim_fixture, ag3_sim_api +@case(tags="af1") def case_af1_sim(af1_sim_fixture, af1_sim_api): return af1_sim_fixture, af1_sim_api +@case(tags="adir1") def case_adir1_sim(adir1_sim_fixture, adir1_sim_api): return adir1_sim_fixture, adir1_sim_api @@ -1076,7 +1081,7 @@ def test_snp_allele_counts_with_site_mask_param(fixture, api: AnophelesSnpData): ) -@parametrize_with_cases("fixture,api", cases=".") +@parametrize_with_cases("fixture,api", cases=".", filter=~ft.has_tag("adir1")) def test_snp_allele_counts_with_sample_query_param(fixture, api: AnophelesSnpData): # Fixed parameters. all_sample_sets = api.sample_sets()["sample_set"].to_list() @@ -1098,7 +1103,7 @@ def test_snp_allele_counts_with_sample_query_param(fixture, api: AnophelesSnpDat ) -@parametrize_with_cases("fixture,api", cases=".") +@parametrize_with_cases("fixture,api", cases=".", filter=~ft.has_tag("adir1")) def test_snp_allele_counts_with_sample_query_options_param( fixture, api: AnophelesSnpData ):