bio::ontologyio::interproparser(3pm) [debian man page]

Bio::OntologyIO::InterProParser(3pm)			User Contributed Perl Documentation		      Bio::OntologyIO::InterProParser(3pm)

NAME

       Bio::OntologyIO::InterProParser - Parser for InterPro xml files.

SYNOPSIS

	   # don't use this module directly - use Bio::OntologyIO with instead
	   my $ipp = Bio::OntologyIO->new( -format  => 'interpro',
					   -file    => 't/data/interpro.xml',
					   -ontology_engine => 'simple' );

DESCRIPTION

	 Use InterProParser to parse InterPro files in xml format. Typical
	 use is the interpro.xml file published by EBI. The xml records
	 should follow the format described in interpro.dtd, although the dtd
	 file is not needed, and the XML file will not be validated against it.

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:

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

AUTHOR - Peter Dimitrov
       Email dimitrov@gnf.org

APPENDIX

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

   new
	Title	: new
	Usage	:
	Function: Initializes objects needed for parsing.
	Example : $ipp = Bio::OntologyIO::InterProParser->new(
					 -file => 't/data/interpro.xml',
					 -ontology_engine => 'simple' )

	Returns : Object of class Bio::OntologyIO::InterProParser.
	Args	:

	 -file		  - file name
	 -ontology_engine - type of ontology engine. Should satisfy the
			    OntologyEngine interface requirements. Currently
			    the only option is 'simple'. In the future
			    Graph.pm based engine will be added to the
			    choices.

   parse
	Title	: parse
	Usage	:
	Function: Performs the actual parsing.
	Example : $ipp->parse();
	Returns :
	Args	:

   next_ontology
	Title	: next_ontology
	Usage	: $ipp->next_ontology()
	Function: Parses the input file and returns the next InterPro ontology
		  available.

		  Usually there will be only one ontology returned from an
		  InterPro XML input.

	Example : $ipp->next_ontology();
	Returns : Returns the ontology as a Bio::Ontology::OntologyEngineI
		  compliant object.
	Args	:

       See Bio::Ontology::OntologyEngineI.

   _is_parsed
	Title	: _is_parsed
	Usage	: $obj->_is_parsed($newval)
	Function:
	Example :
	Returns : value of _is_parsed (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   secondary_accessions_map
	Title	: secondary_accessions_map
	Usage	: $obj->secondary_accessions_map()
	Function: This method is merely for convenience, and one should
		  normally use the InterProTerm secondary_ids method to
		  access the secondary accessions.
	Example : $map = $interpro_parser->secondary_accessions_map;
	Returns : Reference to a hash that maps InterPro identifier to an
		  array reference of secondary accessions following the
		  InterPro xml schema.
	Args	: Empty hash reference

perl v5.14.2							    2012-03-02				      Bio::OntologyIO::InterProParser(3pm)