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)