[Bioperl-l] accessing genbank

Brian Osborne brian_osborne at cognia.com
Thu Jun 3 09:58:22 EDT 2004


You don't want "get_Seq", you want to use "get_Stream" if you're using
multiple ids. Something like:

$seqio = $gb->get_Stream_by_id(["J00522","AF303112","2981014"]);

 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 S.Paul
Sent: Thursday, June 03, 2004 5:51 PM
To: bioperl-l
Subject: [Bioperl-l] accessing genbank

Hi Everybody:

I have been trying to access the Genbank for the following accession numbers
and outfut it to a file and am getting the following error message:
MSG: acc does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
STACK Bio::DB::GenBank::get_Seq_by_acc
STACK toplevel Genbank_seq_dopamine.pl:11

Not sure what I am doing wrong.  I can, however, retrieve individual
accession number.  I am enclosing the code.

Thanks for the help in advance

Sujoy Paul

use Bio::DB::GenBank;
use Bio::SeqIO;
use Bio::DB::WebDBSeqI;
my $gb = new Bio::DB::GenBank;

my $seqio = $gb->get_Seq_by_acc(['AAH21195','AAH38978']);

my $seqout = new Bio::SeqIO(-fh =>'dopamin_human.gbk', -format =>


Sujoy Paul, PRISE Centre, UniS, s.paul at surrey.ac.uk

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