[Bioperl-l] Problem retrieving CDS by Acession #

Ryan Golhar golharam at umdnj.edu
Thu Sep 7 10:32:46 EDT 2006


> On Thursday 07 September 2006 01:09, Ryan Golhar wrote:
> > Hi,
> >
> > I'm using Bio::DB::GenBank::get_Seq_by_acc() passing in a valid 
> > accession #, XM_547879.2, for instance.
> >
> > I get the message in return:
> >
> > -------------------- WARNING ---------------------
> > MSG: acc (gb|XM_547879.2) does not exist
> > ---------------------------------------------------
> >
> > If I go to NCBI, and enter the accession, the GenBank entry 
> comes up. 
> > At first I suspected it was the version number, but removing the 
> > version number still causes the same error.
> >
> > Am I doing something wrong?
> 
> from the Docs for Bio::DB::Genbank:
> 
>     $seq = $gb->get_Seq_by_acc('J00522'); # Accession Number
>     $seq = $gb->get_Seq_by_version('J00522.1'); # Accession.version
>     $seq = $gb->get_Seq_by_gi('405830'); # GI Number
> 
> So, you might try using get_Seq_by_version(....).  I didn't 
> test it, but give 
> that a shot.


get_Seq_by_version() worked.  

That does not explain why get_Seq_by_acc does not work with the primary
part of the accession #.




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