[Bioperl-l] accessing genbank

[S.Paul]

Thanks to Jason and Brian -- it worked.

Sujoy

Sujoy Paul, PRISE Centre, UniS, s.paul at surrey.ac.uk
----- Original Message ----- 
From: "Jason Stajich" <jason at cgt.duhs.duke.edu>
To: "S.Paul" <s.paul at surrey.ac.uk>
Cc: "bioperl-l" <bioperl-l at portal.open-bio.org>
Sent: Thursday, June 03, 2004 7:06 AM
Subject: Re: [Bioperl-l] accessing genbank


> Those are protein accessions- you want to use Bio::DB::GenPept.
>
> Can someone add a FAQ about this?
>
> On Thu, 3 Jun 2004, S.Paul wrote:
>
> > 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
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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