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Question: How to convert between gene ontology file formats
0
gravatar for dgimode
5.5 years ago by
dgimode • 70
dgimode • 70 wrote:

Hi,

I have done annotation on a denovo transcriptome for which I want to do GO term enrichment. Here's the format for the list of GO terms I get:

TR17386    GO:0005737    GO:0005634    
TR27677    GO:0005737    GO:0005524    GO:0006457
TR24529    GO:0005737    GO:0004332    GO:0006096


But I went them in a list with just 2 columns like this:

TR17386    GO:0005737
TR17386    GO:0005634
TR27677    GO:0005737
TR27677    GO:0005524
TR27677    GO:0006457
TR27677    GO:0006950
TR24529    GO:0005737
TR24529    GO:0004332
TR24529    GO:0006096

Is there a script that can help me achieve this?

Thanks,

Davis
rna-seq • 1.6k views
ADD COMMENT • link •
modified 2.5 years ago by Biostar ♦♦ 20 • written 5.5 years ago by dgimode • 70
4
gravatar for Fidel
5.5 years ago by
Fidel • 2.0k
Germany
Fidel • 2.0k wrote:

This should work:

perl -lane '$id = shift(@F); foreach $GO (@F) {print "$id\t$GO"} ' your_file.tab
ADD COMMENT • link written 5.5 years ago by Fidel • 2.0k

Excellent. Thanks for the solutions. The perl one liner worked perfectly. Thank you

ADD REPLY • link written 5.5 years ago by dgimode • 70

Cool. If the solution worked for you, then accept it  ;)

ADD REPLY • link written 5.5 years ago by Fidel • 2.0k
1
gravatar for PoGibas
5.5 years ago by
PoGibas ♦ 4.8k
Vilnius
PoGibas ♦ 4.8k wrote:
# Solution using R

# Packages
# You might need to install them
library(data.table)
library(reshape2)

# Read in
df <- read.table("original.txt", header=FALSE, fill=TRUE)

# Format as wanted
res <- melt(df, id="V1")

# Remove empty row
setDT(res)
res <- res[value != "", list(V1, value)]

# Save as a text file
write.table(res, "wanted.txt", col.names=FALSE, row.names=FALSE, quote=FALSE)
ADD COMMENT • link modified 5.5 years ago • written 5.5 years ago by PoGibas ♦ 4.8k
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