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

Chris Fields cjfields at illinois.edu
Tue Jan 12 18:36:53 EST 2010


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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