[Bioperl-l] Bio::DB::SoapEUtilities : access to Entrez SOAP web service

Chris Fields cjfields at illinois.edu
Tue Jan 12 19:22:10 EST 2010


Okay, just making sure (I was getting a bit paranoid).  Great work on the SOAP interface, BTW!

chris

On Jan 12, 2010, at 6:08 PM, Mark A. Jensen wrote:

> Um, yeah.
> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu>
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: "BioPerl List" <bioperl-l at bioperl.org>
> Sent: Tuesday, January 12, 2010 6:36 PM
> Subject: Re: [Bioperl-l] Bio::DB::SoapEUtilities : access to Entrez SOAP web service
> 
> 
> Um, just to be clear, this isn't Bio::DB::EUtilities, right (it's Bio::DB::SoapEUtilities)?  Otherwise this would be a serious namespace and API conflict with the current EUtilities tools.
> 
> chris
> 
> On Jan 12, 2010, at 11:33 AM, Mark A. Jensen wrote:
> 
>> Hi All--
>> 
>> The beta of Bio::DB::SoapEUtilities is now available in the
>> bioperl-run trunk: one-stop shopping for the NCBI Entrez SOAP web
>> service. The system is fully WSDL based, and all eutils are
>> available. The best thing (IMHO) are the result adaptors, which
>> provide conversion and iteration of SOAP results into BioPerl
>> objects. Schau, mal:
>> 
>> use Bio::DB::EUtilities;
>> my $fac = Bio::DB::EUtilities->new(); # step 1
>> my $seqio = $fac->esearch(
>>      -db => 'nucleotide',
>>      -term => 'HIV1 and CCR5 and Brazil'
>>   )->run(-auto_adapt => 1, -rettype => 'fasta'); # step 2, 3
>> # yes, it's already done the efetch under the hood...
>> while ( my $seq = $seqio->next_seq ) { # step 4
>> # do something with $seq, a Bio::Seq object...
>> }
>> 
>> or this:
>> 
>> my $links = $fac->elink( -db => 'protein',
>>                         -dbfrom => 'nucleotide',
>>                         -id => \@nucids )->run( -auto_adapt => 1 );
>> 
>> # maybe more than one associated id...
>> my @prot_0 = $links->id_map( $nucids[0] );
>> 
>> while ( my $ls = $links->next_linkset ) {
>>   @ids = $ls->ids;
>>   @submitted_ids = $ls->submitted_ids;
>>   # etc.
>> }
>> 
>> and much, much more. See
>> 
>> http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service
>> 
>> and of course, the POD, for all the details, including
>> download/installation. Tests in bioperl-run/t.
>> 
>> cheers,
>> MAJ
>> 
>> -- No new dependencies were added or animals mistreated
>> -- during the making of these modules.
>> 
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>> Bioperl-l at lists.open-bio.org
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> 
> 




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