Extraction of a portion of a fasta header

[chayan]

Hi,

I have a multi fasta file whose header is like below,

">WLPTB:00031:00193;size=517;"

now i want to extract just the "size=517" portion from all the sequences..

any help???

Best,
Chayan

[chayan]

And if possible basicslly i want to extract only the integer "517" after the "size=" portion

thnks

[dariober]

And if possible basicslly i want to extract only the integer "517" after the "size=" portion

thnks

This should do (seq.fa is your fasta file):

grep -P -o 'size=\d+' seq.fa | sed 's/size=//'

[dpryan]

Something like this should work:

grep ">" foo.fasta | cut -d "=" -f 2 | cut -d ";" -f 1

You could also just use biopython or bioperl, which would allow you to more easily keep these values associated with their sequences if that's needed.

[dpryan]

Behold, the usefulness and flexibility of standard unix command line tools!