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

[Mark Wilkinson]

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&rettype=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&rettype=gb&db=nucleotide&tool=bioperl&id=J00522&usehistory=n


Help please :-)

Cheers all!

M


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