Fields, Christopher J | 16 Sep 16:39 2013

Re: GI to taxonomy

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
> 
> 
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Gmane