Bio::DB::SoapEUtilities::FetchAdaptor - Conversion of Entrez SOAP messages to BioPerl objects


 $fac = Bio::DB::SoapEUtilities->new();
 $soap_result = $fac->efetch( -db => 'protein', -id => 2597988 );
 $adp = Bio::DB::SoapEUtilities::FetchAdaptor(
         -result => $soap_result,
         -type => 'seq'
 while ( $gb_seq = $adp->next_obj ) {
    # do stuff


FetchAdaptor is the base class of a system, modeled after Bio::SeqIO, to parse SOAP responses from the NCBI Entrez efetch utility into germane BioPerl objects.

The user will rarely need to instantiate a FetchAdaptor with Bio::DB::SoapEUtilities::Result object as in the "SYNOPSIS". It usually suffices to use the -auto_adapt parameter in the factory run() method:

 my $fac = Bio::DB::SoapEUtilities->new();
 my $taxio = $fac->efetch(-db => 'taxonomy', -id => 1394)->run(-auto_adapt=>1);
 my $sp = $taxio->next_species; # Bio::Species objects
 my $seqio = $fac->efetch(-db => 'protein', -id => 730439)->run(-auto_adapt=>1);
 my $seq = $seqio->next_seq; # Bio::Seq::RichSeq objects


Bio::DB::SoapEUtilities, FetchAdaptor subclasses


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

AUTHOR - Mark A. Jensen

Email maj -at- fortinbras -dot- us


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $obj = new Bio::DB::SoapEUtilities::FetchAdaptor();
 Function: Builds a new Bio::DB::SoapEUtilities::FetchAdaptor object
 Returns : an instance of Bio::DB::SoapEUtilities::FetchAdaptor
 Args    : named arguments
           -som => $soap_som_object (soap message)
           -type => $type ( optional, forces loading of $type adaptor )


 Title   : _initialize
 Usage   : 
 Returns : 
 Args    : 


 Title   : _load_adaptor
 Usage   : 
 Function: loads a FetchAdaptor subclass
 Returns : 
 Args    : adaptor type (subclass name)


 Title   : obj_class
 Usage   : $adaptor->obj_class
 Function: Returns the fully qualified BioPerl classname
           of the objects returned by next_obj()
 Returns : scalar string (class name)
 Args    : none


 Title   : next_obj
 Usage   : $obj = $adaptor->next_obj
 Function: Returns the next parsed BioPerl object from the 
 Returns : object of class obj_class()
 Args    : none


 Title   : rewind
 Usage   : 
 Function: Rewind the adaptor's iterator
 Returns : 
 Args    : none


 Title   : result
 Usage   : 
 Function: contains the SoapEUtilities::Result object
 Returns : Bio::DB::SoapEUtilities::Result object
 Args    : none


 Title   : type
 Usage   : 
 Function: contains the fetch type of this adaptor
 Returns : 
 Args    :