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How can I extract protein sequence from gff file?

I have a gff file containing genes predicted by AUGUSTUS, the file already containing CDS, exons, and protein sequences. I need to extract protein sequence from the file using bash.

sequence bash gff
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updated by drew.b.ferrell • drew.b.ferrell • written by amal.elzemrany • amal.elzemrany

You can use awk. Replace 1 with the column number where your sequences are.

awk '{print $1}' my.GFF
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written by drew.b.ferrell • drew.b.ferrell

Please do not post the images of the data instead of posting data.

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written by cpad0112 cpad0112

1 answer

Oh, I see. Strange, and more complicated output. Not impossible though. I'm assuming you want the hash (#) and space removed from the beginning of each protein sequence as well.

Let me know if this does the trick for you:

 awk '/# protein sequence/{a=1}/# Evidence/{a=0}a' Genes.gff | sed 's/# //'
  • /# protein sequence/ matches lines having this text, as well as /# Evidence/ does.
  • /# protein sequence/{a=1} sets the flag when the text # protein sequence is found.
  • /# Evidence/{a=0} unsets the flag when the text /# Evidence is found.
  • The final a is a pattern with the default action, which is to print $0: if flag is equal 1 the line is printed.
  • Finally, sed removes the hash and space from the beginning of each line.
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written by drew.b.ferrell • drew.b.ferrell

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