Fields, Christopher J | 16 Sep 17:14 2013

Re: GI to taxonomy

Just tested it and it seems to work fine (passes tests).  I committed a change to both the master and 1.6 branches.

chris

On Sep 16, 2013, at 9:58 AM, Bernd W <bernd.web <at> gmail.com> wrote:

> Hi Chris, Brian,
> 
> Indeed, according to NCBI docs
> (http://www.ncbi.nlm.nih.gov/books/NBK25500/), the base URL should be:
> 
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/
> 
> 
> Example seach:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=science[journal]+AND+breast+cancer+AND+2008[pdat]
> 
> 
> Kind regards,
> Bernd
> 
> On Mon, Sep 16, 2013 at 4:39 PM, 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
>>> 
>>> 
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>> 
>> 
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Gmane