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Filtering fasta file based on identifier

Hi, I have a fasta file with many segments and I want to filter out all the segments that have a "P" in the identifier of the segment. Is there a conventional way to do so? Thanks.

fasta filter
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updated by Ram Ram • written by jyu429 jyu429

Thank you!

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updated by Ram Ram • written by jyu429 jyu429

2 answers 

bioawk -c fastx '$name ~ /P/ { print ">"$name; print $seq }' <sequences.fa

If you wanna take all except those with a "P",

bioawk -c fastx '$name ! /P/ { print ">"$name; print $seq }' <sequences.fa

bioawk here

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written by Ram Ram

Neat. I've not found a use for bioawk before but this seems perfect.

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written by Matt Shirley Matt Shirley

It kinda clicked out of the blue for me yesterday. Now I'm gonna add this to my arsenal of regular-use tools :-)

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written by Ram Ram

how can give the transcriptome.fasta and headerlist.txt in this command?

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written by Shahzad • Shahzad

What are those two files?

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written by Ram Ram

just awk

awk '/^>/{N=0} /^>P/{N=1} {if(N)print}' *.fa
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Maybe

/^>\S*P\S*/

To match identifiers (up to the first space) that contain P rather than just identifiers that start with P.

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updated by Ram Ram • written by Rob Syme Rob Syme

Would this not print only headers, Pierre?

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written by Ram Ram

no, if there is no 'next' statement, awk continues to scan all the patterns.

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written by Pierre Lindenbaum Pierre Lindenbaum

Oops, I read it wrong. I read it as the if(N) print being in the same {} as the N=1. My bad!

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written by Ram Ram

But where does the ouput go? Sorry for my ignorance.

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written by jahn.davik • jahn.davik

"standard out" or "stdout". You can redirect this to a file like:

awk '/^>/{N=0} /^>P/{N=1} {if(N)print}' *.fa > out.fa
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written by Matt Shirley Matt Shirley

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