Mercurial > repos > proteore > proteore_id_converter
diff id_converter_UniProt.R @ 4:134949593a3b draft
planemo upload commit 4af7ac25de19ca10b1654820e909c647a2d337b2-dirty
| author | proteore |
|---|---|
| date | Mon, 19 Mar 2018 09:58:17 -0400 |
| parents | f2d0b13d9615 |
| children | 0584344186eb |
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--- 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