Merge branch 'master' into master

Author: pwrose

example1/3-FitModel.html

@@ -12067,10 +12067,11 @@ <h2 id="Select-a-Classification-Method-(default-SVM)">Select a Classification Me
 
 
 
-<div id="6b3611d1-e0af-421e-b0f1-f0df1e9309d2"></div>
+
+<div id="b13aa3da-a92c-4ae9-af15-c6d66b025b16"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#6b3611d1-e0af-421e-b0f1-f0df1e9309d2');
+var element = $('#b13aa3da-a92c-4ae9-af15-c6d66b025b16');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "ab03394bfe0b457ea53b160d07957fc3", "version_major": 2, "version_minor": 0}

example1/4-Predict.html

@@ -11855,10 +11855,10 @@ <h2 id="Enter-a-Protein-Sequence-in-Text-Box">Enter a Protein Sequence in Text B
 
 
 
-<div id="e25fe3ca-d369-498b-84b3-ff010d88ef5f"></div>
+<div id="09051c6c-3269-45c9-bde1-ad39c3085667"></div>
 <div class="output_subarea output_widget_view ">
 <script type="text/javascript">
-var element = $('#e25fe3ca-d369-498b-84b3-ff010d88ef5f');
+var element = $('#09051c6c-3269-45c9-bde1-ad39c3085667');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
 {"model_id": "9bef296ce825422592439bdcd9ad4e96", "version_major": 2, "version_minor": 0}

example2/0-Workflow.html

@@ -11948,18 +11948,18 @@ <h2 id="Version-and-Hardware-Information">Version and Hardware Information<a cla
 
 
 <div class="output_subarea output_stream output_stdout output_text">
-<pre>CPython 3.6.3
-IPython 6.3.1
+<pre>CPython 3.7.0
+IPython 6.4.0
 
 matplotlib 2.2.2
 pyvolve 0.8.8
 seaborn 0.9.0
 treesap n
 treeswift n
 
-compiler   : GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)
+compiler   : Clang 9.1.0 (clang-902.0.39.2)
 system     : Darwin
-release    : 17.5.0
+release    : 17.7.0
 machine    : x86_64
 processor  : i386
 CPU cores  : 4

example2/0-Workflow.ipynb

@@ -146,18 +146,18 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPython 3.6.3\n",
-      "IPython 6.3.1\n",
+      "CPython 3.7.0\n",
+      "IPython 6.4.0\n",
       "\n",
       "matplotlib 2.2.2\n",
       "pyvolve 0.8.8\n",
       "seaborn 0.9.0\n",
       "treesap n\u0007\n",
       "treeswift n\u0007\n",
       "\n",
-      "compiler   : GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)\n",
+      "compiler   : Clang 9.1.0 (clang-902.0.39.2)\n",
       "system     : Darwin\n",
-      "release    : 17.5.0\n",
+      "release    : 17.7.0\n",
       "machine    : x86_64\n",
       "processor  : i386\n",
       "CPU cores  : 4\n",
@@ -198,7 +198,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.3"
+   "version": "3.7.0"
   }
  },
  "nbformat": 4,

example2/1-SimulateTree.html

@@ -0,0 +1,63 @@
+#!/usr/bin/env python3
+'''
+Helper functions for Example 2: "Simulate Phylogenetic Trees and Sequences"
+'''
+from math import log
+
+def read_FASTA(filename):
+    '''
+    Given the name of a FASTA file, parse the contents of the FASTA file and return a dictionary in which keys are identifiers and values are sequences.
+    '''
+    seqs = {}
+    name = None
+    seq = ''
+    f = open(filename)
+    for line in f:
+        l = line.strip()
+        if len(l) == 0:
+            continue
+        if l[0] == '>':
+            if name is not None:
+                assert len(seq) != 0, "Malformed FASTA"
+                seqs[name] = seq
+            name = l[1:]
+            assert name not in seqs, "Duplicate sequence ID: %s" % name
+            seq = ''
+        else:
+            seq += l
+    f.close()
+    assert name is not None and len(seq) != 0, "Malformed FASTA"
+    seqs[name] = seq
+    return seqs
+
+def distance_matrix_to_list(dm):
+    '''
+    Convert an n-by-n pairwise distance matrix (dictionary of dictionaries) into a list of n(n-1)/2 pairwise distances. Sorts keys in ascending order.
+    '''
+    keys = sorted(dm.keys())
+    return [dm[keys[i]][keys[j]] for i in range(len(keys)-1) for j in range(i+1,len(keys))]
+
+def hamming(u,v):
+    '''
+    Given a pair of sequences u and v with equal lengths, compute the Hamming distance between u and v (as a proportion, not a count).
+    '''
+    return sum(u[i] != v[i] for i in range(len(u)))/float(len(u))
+
+def compute_hamming_distance_matrix(sequences):
+    '''
+    Given a dictionary of n sequences in which keys are identifiers and values are sequences, return an n-by-n pairwise distance matrix (dictionary of dictionaries) of Hamming distances.
+    '''
+    return {u:{v:hamming(sequences[u],sequences[v]) for v in sequences} for u in sequences}
+
+def jc69_correction(h):
+    '''
+    Given a Hamming distance h, compute the corresponding JC69-corrected phylogenetic distance.
+    '''
+    return -3*log(1-(4*h/3))/4
+
+def compute_jc69_corrected_distance_matrix(sequences):
+    '''
+    Given a dictionary of n sequences in which keys are identifiers and values are sequences, return an n-by-n pairwise distance matrix (dictionary of dictionaries) of JC69-corrected distances.
+    '''
+    hamming_distances = compute_hamming_distance_matrix(sequences)
+    return {u:{v:jc69_correction(hamming_distances[u][v]) for v in sequences} for u in sequences}

example2/1-SimulateTree.ipynb

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