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Bio::OntologyIO::dagflat.3pm

NAME

Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats

SYNOPSIS

   use Bio::OntologyIO;
 
   # do not use directly -- use via Bio::OntologyIO
   # e.g., the GO parser is a simple extension of this class
   my $parser = Bio::OntologyIO->new
         ( -format       => "go",
      -defs_file    => "/home/czmasek/GO/GO.defs",
           -files        => ["/home/czmasek/GO/component.ontology",
                             "/home/czmasek/GO/function.ontology",
                             "/home/czmasek/GO/process.ontology"] );
 
   my $go_ontology = $parser->next_ontology();
 
   my $IS_A       = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
   my $PART_OF    = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
   my $RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );
 
 

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

Christian M. Zmasek

Email: czmasek-at-burnham.org or cmzmasek@yahoo.com

WWW: http://monochrome-effect.net/

Address:

   Genomics Institute of the Novartis Research Foundation
   10675 John Jay Hopkins Drive
   San Diego, CA 92121
 
 

CONTRIBUTOR

  Hilmar Lapp, hlapp at gmx.net
 
 

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 => "go",
                              -defs_file => "/path/to/GO.defs",
                              -files => ["/path/to/component.ontology",
                                         "/path/to/function.ontology",
                                         "/path/to/process.ontology"] );
  Function: Creates a new dagflat parser.
  Returns : A new dagflat parser object, implementing Bio::OntologyIO.
  Args    : -defs_file  => the name of the file holding the term
                           definitions
            -files      => a single ontology flat file holding the
                           term relationships, or an array ref holding
                           the file names (for GO, there will usually be
                           3 files: component.ontology, function.ontology,
                           process.ontology)
            -file       => if there is only a single flat file, it may
                           also be specified via the -file parameter
            -ontology_name => the name of the ontology; if not specified the
                           parser will auto-discover it by using the term
                           that starts with a $, and converting underscores
                           to spaces
            -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 undef if
            there is no more ontology in the input.
  Args    :
 
 

defs_file

  Title   : defs_file
  Usage   : $parser->defs_file( "GO.defs" );
  Function: Set/get for the term definitions filename.
  Returns : The term definitions file name [string].
  Args    : On set, the term definitions file name [string] (optional).
 
 

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
 
 

_flat_files

  Title   : _flat_files
  Usage   : $files_to_parse = $parser->_flat_files();
  Function: Get the array of ontology flat files that need to be parsed.
 
            Note that this array will decrease in elements over the
            parsing process. Therefore, it\'s value outside of this
            module will be limited. Also, be careful not to alter the
            array unless you know what you are doing.
 
  Returns : a reference to an array of zero or more strings
  Args    : none
 
 

_defs_io

  Title   : _defs_io
  Usage   : $obj->_defs_io($newval)
  Function: Get/set the Bio::Root::IO instance representing the
            definition file, if provided (see defs_file()).
  Example :
  Returns : value of _defs_io (a Bio::Root::IO object)
  Args    : on set, new value (a Bio::Root::IO object or undef, optional)