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:

         https://github.com/bioperl/bioperl-live/issues

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)