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I am trying to edit the "end" of my sequences in a GFF3 that contains 10000 sequences (so I do not want to do it manually). I want to add 30 residues to every single fragment. How can I do this?

Currently, I have a file that looks like this:

##gff-version 3
sp_P45452_MMP13_HUMAN   SignalP-5.0 signal_peptide  1   19  0.994300    .   .   .
sp_Q8R2H5_PHLD_RAT      SignalP-5.0 signal_peptide  1   23  0.986089    .   .   .

I would like to edit it so that it looks like this:

##gff-version 3
sp_P45452_MMP13_HUMAN   SignalP-5.0 signal_peptide  1   49  0.994300    .   .   .
sp_Q8R2H5_PHLD_RAT      SignalP-5.0 signal_peptide  1   53  0.986089    .   .   .

Thank you!

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That's what awk excels at! Simply set the input (-F '\t') and output (-v OFS='\t') record field separators to tab, and add 30 to the value of the fifth field on lines that don't start with a #:

$ awk -F'\t' -v OFS='\t' '/^[^#]/{$5+=30}1' file.gtf 
##gff-version 3
sp_P45452_MMP13_HUMAN   SignalP-5.0 signal_peptide  1   19  30.9943 .   .   .
sp_Q8R2H5_PHLD_RAT  SignalP-5.0 signal_peptide  1   23  30.9861 .   .   .
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  • $\begingroup$ yep this is the good stuff $\endgroup$
    – Pallie
    Sep 16 at 13:50
  • $\begingroup$ Thank you so much! I am new to awk and this was super helpful! $\endgroup$
    – obsmith
    Sep 16 at 13:51

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