[EMBOSS] Antwort: extractseq

[david.bauer at bayerhealthcare.com]

Hi ZL,

the input for extracseq is 'sequence' and not 'seqall' so it works only on 
 a single sequence.

You could use something like this to loop through your multiple fasta file 
(the example returns the first 30 bases of each of 3 sequences contained 
in test.fa).

perl -e 'for($I=0;$I<3;$I++){$seq = `skipseq test.fa -skip $I | seqret 
-filter -firstonly | extractseq -filter -region 1-30`; print $seq}'

Cheers,
David.


emboss-bounces at lists.open-bio.org schrieb am 11/24/2009 06:16:07 PM:

> Dear EMBOSS Users,
> 
> Is it possible to use extractseq to extract multiple regions from a 
> multi-fasta file according the headers? Thank you.
> 
> Cheers,
> ZL
> 
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