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Using awk or sed to edit a column in a gtf file

Dear all,

I have a gft file and I want to remove a cenrtaind word in a certain column:

In this case I want to remove in the second column "mRNA." and just to keep CA01g00010 in this column, could you help me with this?

Pepper1.55ch01  mRNA.CA01g00010 63209   63880

I would like this output 

Pepper1.55ch01   CA01g00010 63209   63880

Best

awk sed gft linux
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updated by GouthamAtla GouthamAtla • written by imda • imda

In the case provided it can also be: sed "s/\tmRNA\./\t/g" example.gtf.

• 0 views • link
written by AK AK

1 answer 

awk -v OFS="\t" -v FS="\t" '{ $2=gensub("^mRNA.", "", 0, $2); print $0; }' your_file > your_modified_file

Edit: removed tab-separated assumption, as I just saw it should treat a gtf, which we all know is tab-separated.

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written by cschu181 cschu181

another awk solution:

$ awk -v OFS="\t" -F "\t" '{sub("^[a-zA-Z]+\.","",$2)}1' test.txt
$ awk -v OFS="\t" -F "\t" '{$2=substr($2,6)}1' test.txt
Pepper1.55ch01  CA01g00010  63209   63880

with gawk installed: 

 $ awk -v OFS="\t" -F "\t" '{sub("^[a-zA-Z]{4}.","",$2)}1' test.txt
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written by cpad0112 cpad0112

This worked awesome for me thank you!

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written by imda • imda

thank you, I could remove mRNA part

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written by imda • imda

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