[Bioperl-l] accessing genbank

[Jason Stajich]

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