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

Mark Wilkinson markw at illuminae.com
Thu Jul 3 00:03:35 EDT 2003

Hi Hilmar, 

Try that bit of code - I've followed it in the debugger and it does
query the protein database.  As far as I can tell, it is hard-coded to
do so by default - the defaults for 'simple', and 'batch' and so on are
all db=>'protein'

I notice that Boulder::Genbank also broke as of Friday.  I've tracked
down the line in that module that is causing the problems and now I have
it working again, but I think GB must have tweaked their interface last
week.  Prior to this, the query sent out by Boulder::Genbank defaulted
to db=n, but that stopped working on Friday around noon.  It now must
make it explicitly db=nucleotide in order for Boulder:Genbank to work. 
I'm sending the bug report and patch to Lincoln, but he's at the
C.elegans meeting so it might not get fixed for a while (if he confirms
that the error is what I believe it is)


On Wed, 2003-07-02 at 16:44, Hilmar Lapp wrote:
> 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>

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