Raw content of Bio::OntologyIO::goflat
<![CDATA[# $Id: goflat.pm,v 1.1.2.3 2003/05/27 22:00:52 lapp Exp $
#
# BioPerl module for Bio::OntologyIO::goflat
#
# Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com>
#
# (c) Christian M. Zmasek, czmasek@gnf.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
goflat - a parser for the Gene Ontology flat-file format
=head1 SYNOPSIS
use Bio::OntologyIO;
# do not use directly -- use via Bio::OntologyIO
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" );
=head1 DESCRIPTION
Needs Graph.pm from CPAN.
This is essentially a very thin derivation of the dagflat parser.
=head1 FEEDBACK
=head2 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://bio.perl.org/MailList.html - About the mailing lists
=head2 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
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR
Christian M. Zmasek
Email: czmasek@gnf.org or cmzmasek@yahoo.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
=head2 CONTRIBUTOR
Hilmar Lapp, hlapp at gmx.net
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::OntologyIO::goflat;
use vars qw( @ISA );
use strict;
use Bio::Ontology::TermFactory;
use Bio::OntologyIO::dagflat;
use constant TRUE => 1;
use constant FALSE => 0;
@ISA = qw( Bio::OntologyIO::dagflat );
=head2 new
Title : new
Usage : $parser = Bio::OntologyIO->new(
-format => "go",
-defs_file => "/path/to/GO.defs",
-files => ["/path/to/component.ontology",
"/path/to/function.ontology",
"/path/to/process.ontology"] );
Function: Creates a new goflat parser.
Returns : A new goflat parser object, implementing L<Bio::OntologyIO>.
Args : -defs_file => the name of the file holding the term
definitions
-files => a single ontology flat file holding the
term relationships, or an array ref holding
the file names (for GO, there will usually be
3 files: component.ontology, function.ontology,
process.ontology)
-file => if there is only a single flat file, it may
also be specified via the -file parameter
-ontology_name => the name of the ontology; if not specified the
parser will auto-discover it by using the term
that starts with a '$', 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.
=cut
# in reality, we let OntologyIO::new do the instantiation, and override
# _initialize for all initialization work
sub _initialize {
my ($self, @args) = @_;
$self->SUPER::_initialize( @args );
# default term object factory
$self->term_factory(Bio::Ontology::TermFactory->new(
-type => "Bio::Ontology::GOterm"))
unless $self->term_factory();
} # _initialize
1;
]]>