Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::DB::SoapEUtilitieUsereContributedBPo::DB::SoapEUtilities::FetchAdaptor(3)

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

SYNOPSIS
	$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
	}

DESCRIPTION
       "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

SEE ALSO
       Bio::DB::SoapEUtilities,	"FetchAdaptor" subclasses

FEEDBACK
   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.

	 bioperl-l@bioperl.org			- General discussion
       http://bioperl.org/wiki/Mailing_lists  -	About the mailing lists

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

       bioperl-l@bioperl.org

       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:

	 http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark A. Jensen
       Email maj -at- fortinbras -dot- us

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

   new
	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 )

   _initialize()
	Title	: _initialize
	Usage	:
	Function:
	Returns	:
	Args	:

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

   obj_class()
	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

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

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

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

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

perl v5.32.1			  2021Bio::DB::SoapEUtilities::FetchAdaptor(3)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | FEEDBACK | AUTHOR - Mark A. Jensen | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::DB::SoapEUtilities::FetchAdaptor&sektion=3&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help