[Bioperl-l] accessing genbank

[Brian Osborne]

Sujoy,

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
C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm:1
7
STACK Bio::DB::GenBank::get_Seq_by_acc
C:/Perl/site/lib/Bio/DB/GenBank.pm:216
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 =>
'genbank');

****************************************************************************
*******************

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