Merge pull request #341 from jotech/master

zachary-foster · web-flow · commit aeea7bc50499 · 2022-07-13T09:31:46.000-07:00
Update parsers.R
diff --git a/R/parsers.R b/R/parsers.R
@@ -61,7 +61,7 @@ parse_phyloseq <- function(obj, class_regex = "(.*)",
   # Parse sample data
   if (! is.null(obj@sam_data)) {
     sam_data <- as.data.frame(as.list(obj@sam_data), stringsAsFactors = FALSE)
-    if (! is.null(rownames(obj@sam_data))) {
+    if (! is.null(rownames(obj@sam_data)) & !"sample_id" %in% colnames(obj@sam_data)) {
       sam_data <- cbind(sample_id = rownames(obj@sam_data), sam_data)
     }
     sam_data[] <- lapply(sam_data, as.character)

Original file line number	Diff line number	Diff line change
`@@ -61,7 +61,7 @@ parse_phyloseq <- function(obj, class_regex = "(.*)",`
`61`	`61`	`# Parse sample data`
`62`	`62`	`if (! is.null(obj@sam_data)) {`
`63`	`63`	`sam_data <- as.data.frame(as.list(obj@sam_data), stringsAsFactors = FALSE)`
`64`		`- if (! is.null(rownames(obj@sam_data))) {`
	`64`	`+ if (! is.null(rownames(obj@sam_data)) & !"sample_id" %in% colnames(obj@sam_data)) {`
`65`	`65`	`sam_data <- cbind(sample_id = rownames(obj@sam_data), sam_data)`
`66`	`66`	`}`
`67`	`67`	`sam_data[] <- lapply(sam_data, as.character)`