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

[Lincoln Stein]

Good lord.  I wasn't the one who introduced it, was I?

Lincoln

On Wednesday 02 July 2003 10:20 pm, Hilmar Lapp wrote:
> OK so I traced the history. The string 'protein' as value for parameter
> db was introduced about a year ago (!) in version 1.44 of
> DB::GenBank.pm. It is also present up to 1.2.1 and was only fixed on
> June 10 this year, almost exactly one year later.
>
> For the bioperl humour book of records, the guy who doesn't remember
> how it came in in the first place is the same who introduced it, and
> who recently also fixed it. I guess we're all overworked. This alone is
> worth having a beer together.
>
> I'm sure the only reason it has never come up before for a whole year
> is that it was simply ignored or overridden. If you look at NCBIHelper
> there are actually circumstances under which it gets overridden from a
> query object. I don't have time to track down why at all it worked
> before and what finally exposed it; it could even be the fact that the
> name of the database (gb versus gp) was also submitted to NCBI and that
> that overwrote the choice of protein or nucleotide, but that NCBI now
> changed that.
>
> At any rate, it was a bloody bad bug that amazingly managed to sit
> around silent for a year, and it has been fixed on both main trunk and
> branch. One more reason to get 1.2.2 out ASAP.
>
> 	-hilmar
>
> On Wednesday, July 2, 2003, at 06:42  PM, Jason Stajich wrote:
> > 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

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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