/ 
FAST-1.03
River stage zero No dependents
/ FAST::Bio::OntologyIO::InterProParser

NAME

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

SYNOPSIS

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

 Returns : Object of class FAST::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 FAST::Bio::Ontology::OntologyEngineI
          compliant object.
Args    :

See FAST::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