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

[Jason Stajich]

I'm pretty sure Lincoln has threatended to remove Bio::DB::GenBank from
Bioperl if NCBI changes the interface again...

I really don't see where you have the defaults for 'db'=> 'protein' in
Bioperl - what version of the code are you using.  I think remember a
release having that bug but I see 'db' => 'nucleotide' on both main trunk
and the branch.

-jason

On Wed, 2 Jul 2003, Mark Wilkinson wrote:

> 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)
>
> M
>
>
> 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
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu