This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Reduce the headers in a fasta file to just the gi number?

I simply want to reduce the headers in a fasta file from the long version below to simply the gi. i.e.

>gi|103058628|gb|DQ517338.1| Staphylococcus phage 80alpha, complete sequence
AGGTATCTGCATAGTTATTCCGAACTTCCAATTAATAAAACTCTATACCCGTAATCTTCAATGAGTTCTG
GCGCTTCCCTTTAATTCCTTTTACATATTCAAAATGAATGTTTTTGATTGCCATCTTTATGAATTCAGTT
TTTAACTCATCTTCCATTAATTCCCAGCCGTTTAGCAATGAATACTTGAAATTTTTAATCTTCTCATAGT

To:

>103058628
AGGTATCTGCATAGTTATTCCGAACTTCCAATTAATAAAACTCTATACCCGTAATCTTCAATGAGTTCTG
GCGCTTCCCTTTAATTCCTTTTACATATTCAAAATGAATGTTTTTGATTGCCATCTTTATGAATTCAGTT
TTTAACTCATCTTCCATTAATTCCCAGCCGTTTAGCAATGAATACTTGAAATTTTTAATCTTCTCATAGT

I'm guessing awk or grep has the technology!

fasta grep awk
• 3,796 views • link
updated by Ram Ram • written by oliver.bayfield • oliver.bayfield

Tip: awk and grep extract things, sed alters things. See Pierre's answer.

• 0 views • link
written by Neilfws Neilfws

1 answer

just sed:

sed 's/^>gi|\([0-9]*\)|.*/>\1/' < in.fasta
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

How can I do it If I need both gi and gb numbers like >gi|103058628|gb|DQ517338.1|?

• 0 views • link
updated by Ram Ram • written by tcf.hcdg tcf.hcdg

Log in to answer this question.

More posts like this