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

Mark A. Jensen maj at fortinbras.us
Tue Jan 12 12:33:30 EST 2010


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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