- AUTHOR - Peter Dimitrov
Bio::OntologyIO::InterProParser - Parser for InterPro xml files.
# 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' );
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
Title : parse Usage : Function: Performs the actual parsing. Example : $ipp->parse(); Returns : Args :
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 :
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)
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