Bio::OntologyIO::obo.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::OntologyIO::obo - a parser for OBO flat-file format from Gene Ontology Consortium

SYNOPSIS

   use Bio::OntologyIO;
 
   # do not use directly -- use via Bio::OntologyIO
   my $parser = Bio::OntologyIO->new
         ( -format       => "obo",
           -file        =>  "gene_ontology.obo");
 
   while(my $ont = $parser->next_ontology()) {
   print "read ontology ",$ont->name()," with ",
                scalar($ont->get_root_terms)," root terms, and ",
                scalar($ont->get_all_terms)," total terms, and ",
                scalar($ont->get_leaf_terms)," leaf terms\n";
   }
 
 

DESCRIPTION

Needs Graph.pm from CPAN.

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 lists 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 the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR

Sohel Merchant

Email: s-merchant@northwestern.edu

Address:

   Northwestern University
   Center for Genetic Medicine (CGM), dictyBase
   Suite 1206,
   676 St. Clair st
   Chicago IL 60611
 
 

CONTRIBUTOR

  Hilmar Lapp, hlapp at gmx.net
  Chris Mungall,   cjm at fruitfly.org
 
 

APPENDIX

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

new

  Title   : new
  Usage   : $parser = Bio::OntologyIO->new(
                              -format => "obo",
                              -file => "gene_ontology.obo");
  Function: Creates a new dagflat parser.
  Returns : A new dagflat parser object, implementing Bio::OntologyIO.
  Args    : -file      => a single ontology flat file holding the
                           terms, descriptions and relationships
            -ontology_name => the name of the ontology; if not specified the
                           parser will assign the name of the ontology as the
                           default-namespace header value from the OBO file.
            -engine     => the Bio::Ontology::OntologyEngineI object
                           to be reused (will be created otherwise); note
                           that every Bio::Ontology::OntologyI will
                           qualify as well since that one inherits from the
                           former.
 
 

See Bio::OntologyIO.

ontology_name

  Title   : ontology_name
  Usage   : $obj->ontology_name($newval)
  Function: Get/set the name of the ontology parsed by this module.
  Example :
  Returns : value of ontology_name (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

parse

  Title   : parse()
  Usage   : $parser->parse();
  Function: Parses the files set with "new" or with methods
            defs_file and _flat_files.
 
            Normally you should not need to call this method as it will
            be called automatically upon the first call to
            next_ontology().
 
  Returns : Bio::Ontology::OntologyEngineI
  Args    :
 
 

next_ontology

  Title   : next_ontology
  Usage   :
  Function: Get the next available ontology from the parser. This is the
            method prescribed by Bio::OntologyIO.
  Example :
  Returns : An object implementing Bio::Ontology::OntologyI, and nothing if
            there is no more ontology in the input.
  Args    :
 
 

close

  Title   : close
  Usage   :
  Function: Closes this ontology stream and associated file handles.
 
            Clients should call this method especially when they write
            ontologies.
 
            We need to override this here in order to close the file
            handle for the term definitions file.
 
  Example :
  Returns : none
  Args    : none