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

Mark A. Jensen maj at fortinbras.us
Tue Jan 12 20:09:28 EST 2010


corrected:

use Bio::DB::SoapEUtilities;
my $fac = Bio::DB::SoapEUtilities->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...
 }

----- Original Message ----- 
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "Chris Fields" <cjfields at illinois.edu>
Cc: "BioPerl List" <bioperl-l at bioperl.org>
Sent: Tuesday, January 12, 2010 7:08 PM
Subject: Re: [Bioperl-l] Bio::DB::SoapEUtilities : access to Entrez SOAP 
webservice


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