Provided by: libbio-perl-perl_1.7.2-2_all bug


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


         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/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" );


       Needs from CPAN.


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       Christian M. Zmasek

       Email:  or



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

        Hilmar Lapp, hlapp at


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

        Title   : new
        Usage   : $parser = Bio::OntologyIO->new(
                                    -format => "go",
                                    -defs_file => "/path/to/GO.defs",
                                    -files => ["/path/to/component.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
                  -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,
                  -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

       See Bio::OntologyIO.

        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)

        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

        Returns : [Bio::Ontology::OntologyEngineI]
        Args    :

        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    :

        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).

        Title   : close
        Usage   :
        Function: Closes this ontology stream and associated file handles.

                  Clients should call this method especially when they write

                  We need to override this here in order to close the file
                  handle for the term definitions file.

        Example :
        Returns : none
        Args    : none

        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

        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)