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

[Mark A. Jensen]

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.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l