[Bioperl-l] Retrieving taxonomy information from a GenBank file

Jason Stajich jason at bioperl.org
Thu Sep 18 17:56:18 EDT 2008


You want the species object ($seq->species)  -- see the Seq HOWTO,  
much of the Seq API is explained.
  http://bioperl.org/wiki/HOWTO:Feature-Annotation#The_Species_Object

-jason
On Sep 18, 2008, at 2:27 PM, ANJAN PURKAYASTHA wrote:

> Hi,
> I'm using the following code to access the "ORGANISM" tag value for  
> the
> record NC_002526.
> I get a value of 0 even though the ORGANISM tag  has a value.  Any  
> idea how
> this might be corrected?
> Thanks.
> Anjan
>
>
> my $gb= new Bio::DB::GenBank;
>
> my $seq = $gb->get_Seq_by_acc('NC_002526');
>
> my $des= $seq->get_tag_values("ORGANISM");
>
> -- 
> =============================
> anjan purkayastha, phd
> bioinformatics analyst
> whitehead institute for biomedical research
> nine cambridge center
> cambridge, ma 02142
>
> purkayas [at] wi [dot] mit [dot] edu
> 703.740.6939
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason at bioperl.org





More information about the Bioperl-l mailing list