Extraction of a portion of a fasta header

chayan · 01-04-2015, 11:51 PM

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 · 01-05-2015, 12:10 AM

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

thnks

dariober · 01-05-2015, 12:49 AM

Quote:

Originally Posted by chayan

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):

Code:

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

dpryan · 01-05-2015, 12:49 AM

Something like this should work:

Code:

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 · 01-05-2015, 12:50 AM

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

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01-04-2015, 11:51 PM	#1
chayan Member Location: USA Join Date: Nov 2012 Posts: 51	Extraction of a portion of a fasta header 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

01-05-2015, 12:49 AM	#4
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	Something like this should work: Code: 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. Last edited by dpryan; 01-05-2015 at 01:25 AM. Reason: Forgot "-f"!

01-05-2015, 12:10 AM	#2
chayan Member Location: USA Join Date: Nov 2012 Posts: 51	And if possible basicslly i want to extract only the integer "517" after the "size=" portion thnks

01-05-2015, 12:50 AM	#5
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	Behold, the usefulness and flexibility of standard unix command line tools!