Bio::OntologyIO::InterProParser.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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