Any script to format headers in fasta files?

Shishir

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Posts: 22
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#1

Any script to format headers in fasta files?

02-05-2013, 07:33 AM

I have a 47GB file to parse. The sequences are in following format:
>TSCS_00041 gene0EA_12345_rframe2_ORF
MLAATHYYKFAIRRLFPLLKDTICASYSISIKHHENFMALSNMPKIWEDVEVDGNNMQWTRFQTTPVMPVYFIAAGVFNLSFITNWNTKLLYRKDILPYMTFAYNVAKNIAWFLSHIRKTKITNHI
>TSCS_00044 gene0EA_12341_rframe2_ORF
MTICASYSISIKHHENFMAIKHHENFMALSNMPKIWEDV
I simply want to format this file like:
>TSCS_00041
MLAATHYYKFAIRRLFPLLKDTICASYSISIKHHENFMALSNMPKIWEDVEVDGNNMQWTRFQTTPVMPVYFIAAGVFNLSFITNWNTKLLYRKDILPYMTFAYNVAKNIAWFLSHIRKTKITNHI
>TSCS_00044
MTICASYSISIKHHENFMAIKHHENFMALSNMPKIWEDV
Could anyone share the script.
Tags: bioinfomatics, fasta format, next gen sequencing, perl, perl script
Richard Finney

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Join Date: Feb 2009

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#2

02-05-2013, 07:45 AM

cut -f1 -d" " inputold.fa > outputnew.fa
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Shishir

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Posts: 22
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#3

02-05-2013, 07:52 AM

Thanks Richard!
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Any script to format headers in fasta files?

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