Split comma seperated list of GO terms into multiple rows and maintain gene identifier in each
I have a tab separated dataset, although the GO terms are comma separated.
GENEID1 GO:XXXXX,GO:YYYYYY,GO:ZZZZZZ
I want to make it so that the dataset becomes a tab-seperated dataset where each GO term is represented on a new line with the gene identifier:
GENEID1 GO:XXXXX
GENEID1 GO:YYYYYY
GENEID1 GO:ZZZZZZ
Many thanks.
3 answers
Do you want to do this in R (possible) or other tools (also possible)?
echo -e "GENEID1\tGO:XXXXX,GO:YYYYYY,GO:ZZZZZZ" > test.txt
in R
library("tidyr")
test <- read.table("test.txt",sep = "\t",header=F)
test
V1 V2
1 GENEID1 GO:XXXXX,GO:YYYYYY,GO:ZZZZZZ
# use tidyr separate rows to convert A1\tGO:1,GO:2 to
# A1 GO:1
# A1 GO:2
test2 <- tidyr::separate_rows(data = test,V2,sep = ",")
test2
V1 V2
1 GENEID1 GO:XXXXX
2 GENEID1 GO:YYYYYY
3 GENEID1 GO:ZZZZZZ
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#!/usr/bin/env python
import sys
with open(sys.argv[1], 'r') as f:
for line in f:
for n in range(len(line.strip().split('\t')[1].split(','))):
print line.strip().split('\t')[0] + 't' + line.strip().split('\t')[1].split(',')[n]
Save as go_tab.py, run as python go_tabl.py input.txt > output.txt
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I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
Is it all tab separated? there are what look like tabs and commas in your example input.
A perl one liner could be
perl -ane '{print map {$F[0]."\t".$_."\n" } @F[1..$#F] }' your_input_file |sed -s 's/,$//'This outputs the same as the input if
your_input_fileis created withecho -e "GENEID1\tGO:XXXXX,GO:YYYYYY,GO:ZZZZZZ" > your_input_file. Might there be a slight typo?