# HG changeset patch
# User proteore
# Date 1521467897 14400
# Node ID 134949593a3bb4f0eedb31708d7fd6be389a59a9
# Parent  72860740f65fdaf36bb263a58730ebd9685dba50
planemo upload commit 4af7ac25de19ca10b1654820e909c647a2d337b2-dirty

diff -r 72860740f65f -r 134949593a3b id_converter_UniProt.R
--- a/id_converter_UniProt.R	Wed Mar 14 10:13:40 2018 -0400
+++ b/id_converter_UniProt.R	Mon Mar 19 09:58:17 2018 -0400
@@ -2,16 +2,16 @@
 readfile = function(filename, header) {
   if (header == "true") {
     # Read only first line of the file as header:
-    headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE)
+    headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
     #Read the data of the files (skipping the first row)
-    file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE)
+    file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
     # Remove empty rows
     file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
     #And assign the header to the data
     names(file) <- headers
   }
   else {
-    file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE)
+    file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
     # Remove empty rows
     file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
   }
@@ -54,7 +54,7 @@
     human_id_mapping_file = args[6]
     
     # Extract ID maps
-    human_id_map = read.table(human_id_mapping_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "")
+    human_id_map = read.table(human_id_mapping_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "", quote = "")
     
     # Extract input IDs
     if (list_id_input_type == "list") {
@@ -105,4 +105,4 @@
 
 mapping()
 
-#Rscript id_converter_UniProt.R "UniProt.AC" "test-data/UnipIDs.txt,c1,false" "file" "Ensembl_PRO,Ensembl,neXtProt_ID" "test-data/output.txt" ../../utils/mapping_file.txt
\ No newline at end of file
+#Rscript id_converter_UniProt.R "UniProt.AC" "test-data/UnipIDs.txt,c1,false" "file" "Ensembl_PRO,Ensembl,neXtProt_ID" "test-data/output.txt" ../../utils/mapping_file.txt