Alexey Morozov | 17 Sep 04:29 2013
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Re: GI to taxonomy

Yes, indeed it is, as Paul pointed out 3 days ago.

2013/9/17 Brian Osborne <bosborne11 <at> verizon.net>

> All,
>
> The problem is "source", as opposed to "-source", as Bernd said.
>
> BIO
>
>
> On Sep 16, 2013, at 11:07 AM, Brian Osborne <bosborne11 <at> verizon.net>
> wrote:
>
> > Chris,
> >
> > Something odd is happening, this can't be right:
> >
> > 161:      $self->_initialize( <at> args);
> > 162==>            return $self;
> > 163   }
> > 164
> > 165
> > 166   sub _initialize {
> > 167:    my($self) = shift;
> > 168
> >  DB<6> p $self->entrez_url
> > source
> >
> > I'll look into this tonight …
> >
> > BIO
> >
> >
> > On Sep 16, 2013, at 10:39 AM, "Fields, Christopher J" <
> cjfields <at> illinois.edu> wrote:
> >
> >> That's possible; there are various eutils interfaces scattered
> throughout bioperl, so it's possible some haven't been updated to the most
> recent URL.  Brian, does a modified URL work?
> >>
> >> chris
> >>
> >> On Sep 16, 2013, at 8:08 AM, Brian Osborne <bosborne11 <at> verizon.net>
> wrote:
> >>
> >>> Chris,
> >>>
> >>> Bio::DB::Taxonomy::entrez uses this URL by default:
> >>>
> >>> http://www.ncbi.nih.gov/entrez/eutils/
> >>>
> >>> Should it be using this one?
> >>>
> >>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/
> >>>
> >>> Brian O.
> >>>
> >>> On Sep 13, 2013, at 4:06 AM, Alexey Morozov <
> alexeymorozov1991 <at> gmail.com> wrote:
> >>>
> >>>> Dear colleagues,
> >>>> I have a bunch of fasta genomes annotated only by their GI numbers,
> and
> >>>> need to get a taxonomy for all of them. So I rewrote get_tree method
> from
> >>>> Bio::DB::Taxonomy:
> >>>>
> >>>> 12 open GIS, GI_FILE;
> >>>> 13 my $tax_db=Bio::DB::Taxonomy->new(source=>'entrez');
> >>>> 14 my $tree;
> >>>> 15 while (<GIS>)
> >>>> 16         {
> >>>> 17         print "Requesting data for GI $_\n";
> >>>> 18         my $taxon=$tax_db->get_taxon(-gi=>"$_",-db=>'nucleotide');
> >>>> 19         if ($ <at> ){die $ <at> ;}#Catch exception and die, just in case
> >>>> 20                 # or die "Cannot get taxonomy data for GI$_:$!\n";
> >>>> 21         if ($tree)
> >>>> 22                 {
> >>>> 23                 $tree->merge_lineage($taxon);
> >>>> 24                 }else
> >>>> 25                 {
> >>>> 26                 $tree=Bio::Tree::Tree->new(-node=>$taxon);
> >>>> 27                 }
> >>>> 28         }
> >>>>
> >>>> This (line 18) way to invoke Bio::DB::Taxonomy->get_taxon is
> documented and
> >>>> I expect to get taxon objects. Yet all I get is
> >>>>
> >>>>
> >>>> --------------------- WARNING ---------------------
> >>>> MSG: Must have provided a valid HASHref for -params
> >>>> ---------------------------------------------------
> >>>> Requesting data for GI 15604717
> >>>>
> >>>>
> >>>> ------------- EXCEPTION: Bio::Root::Exception -------------
> >>>> MSG: Can't query website: 400 URL must be absolute
> >>>> STACK: Error::throw
> >>>> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> >>>> STACK: Bio::DB::Taxonomy::entrez::get_taxon
> >>>> /usr/share/perl5/Bio/DB/Taxonomy/entrez.pm:247
> >>>> STACK: ./get_tax:18
> >>>> -----------------------------------------------------------
> >>>>
> >>>> Directly using Bio::DB::Taxonomy::entrez doesn't help, GI numbers
> load OK,
> >>>> so I have no clue what happened.
> >>>> Need help.
> >>>> --
> >>>> Alexey Morozov,
> >>>> LIN SB RAS, bioinformatics group.
> >>>> Irkutsk, Russia.
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l <at> lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l <at> lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
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> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
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> > Bioperl-l <at> lists.open-bio.org
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>
>

--

-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

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