[Bioperl-l] How do you change the default on Bio::DB::GenBank?

[Hilmar Lapp]

This is strange. DB::GenBank should query the nucleotide databank
whereas DB::GenPept is for querying the protein databank. You use
different modules for the two queries, not the same with a different
initialization parameter.

	-hilmar

> -----Original Message-----
> From: Mark Wilkinson [mailto:markw at illuminae.com] 
> Sent: Wednesday, July 02, 2003 3:32 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] How do you change the default on 
> Bio::DB::GenBank?
> 
> 
> Hi BioPerlers, 
> 
> Can someone tell me how to change the default db name in 
> Bio::DB::GenBank?  I've spent the past two hours in debug 
> mode and can't see any point at which an argument for the 
> database name is even tested
> - it is coded to default to 'protein' which isn't very useful to me. 
> Such a switch doesn't appear anywhere in the documentation 
> either as far as I can tell.  I took a guess and thought the 
> following would work:
> 
> use Bio::DB::GenBank; 
> my $gb = Bio::DB::GenBank->new(-db=>"nucleotide");
> print $gb->get_Seq_by_acc("AF005495");
> 
> But that still sends out a GET request to the protein database:
> 
http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&retty
pe=gb&db=protein&tool=bioperl&id=J00522&usehistory=n

Whereas what I want it to do is:

http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&retty
pe=gb&db=nucleotide&tool=bioperl&id=J00522&usehistory=n


Help please :-)

Cheers all!

M


-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae

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