[Bioperl-l] parsing a list of ids to a fasta file.

Khan, Sohail khan at cshl.edu
Mon Feb 26 15:29:19 EST 2007


Thanks Michael.  I have the scripts installed.  I can pass an id to indexed fasta file and retrieve the seq.  However, I was wondering if I can pass a list of ids from a file and get seq. for all the ids?
Thanks.

-Sohail

-----Original Message-----
From: michael watson (IAH-C) [mailto:michael.watson at bbsrc.ac.uk]
Sent: Tuesday, February 20, 2007 4:33 PM
To: Khan, Sohail; Bioperl-l at lists.open-bio.org
Subject: RE: [Bioperl-l] parsing a list of ids to a fasta file.


Suggest you use Bio::Index::Fasta to create an index for the fasta file and then a simple script to retrieve sequences using that index.  Or just use the pre-written bp_index.PLS and bp_fetch.PLS scripts.
 
http://www.bioperl.org/wiki/Module:Bio::Index::Fasta

________________________________

From: bioperl-l-bounces at lists.open-bio.org on behalf of Khan, Sohail
Sent: Tue 20/02/2007 8:42 PM
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] parsing a list of ids to a fasta file.



Dear list,

I am new to Bio-Perl.  I have the following question:
I have a list of ids, which I would like to parse against a large fasta file to retrieve the Seq for parsed ids.  I appreciate any suggestions.
Thanks.

Khan



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