[Bioperl-l] Getting entire descriptions from FASTA files

[Brian Osborne]

David,

$seq_in->display_id and $seq_in->desc together should constitute the entire
line - you're not seeing this?


Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of David García
Cortés
Sent: Wednesday, January 12, 2005 6:36 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Getting entire descriptions from FASTA files


Hello.

I want to get the entire description line in FASTA format (i mean:
description, accession number, etc...). Ive tried with display_id this way:

my $seq_inIO     = Bio::SeqIO->new(-file => "$proteasa",
                         -format => 'Fasta');

my $seq_in        = $seq_inIO->next_seq();

my $id_peptid = $seq_in->display_id;

but I only obtain the gi and gb numbers, not the description line.

Then, I tried with $seq_in->desc instead of $seq_in->display_id , but then I
only obtain the description (or part of it).

Is there a way to get the entire description line the same way you see it at
the FASTA file?

Thanks.

--
David García Cortés
Instituto Nacional de Bioinformática (INB)
Nodo Computacional GNHC-2 UPC-CIRI
c/. Jordi Girona 1-3
Modul C6-E201                   Tel.  : 934 011 650
E-08034 Barcelona               Fax   : 934 017 014
Catalunya (Spain)               e-mail: davidg at lsi.upc.edu


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