Raw content of Bio::OntologyIO::soflat # $Id: soflat.pm,v 2003/05/27 22:00:52 lapp Exp $ # # BioPerl module for Bio::OntologyIO::soflat # # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com> # # (c) Christian M. Zmasek, czmasek@gnf.org, 2002. # (c) Hilmar Lapp, hlapp at gnf.org, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002-3. # # 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 soflat - a parser for the Sequence Ontology flat-file format =head1 SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "so", # or soflat -defs_file => "/home/czmasek/SO/SO.defs", -file => "/home/czmasek/SO/sofa.ontology" ); my $sofa_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 base-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::soflat; 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 : $parser = Bio::OntologyIO->new( -format => "soflat", -files => ["/path/to/sofa.ontology"] ); Function: Creates a new soflat parser. Returns : A new soflat parser object, implementing Bio::OntologyIO. Args : -defs_file => the name of the file holding the term definitions -files => a single ontology flat file holding the term relationships, or an array ref holding the file names -file => if there is only a single flat file, it may also be specified via the -file parameter -ontology_name => the name of the ontology; if not specified the parser will auto-discover it by using the term that starts with a '$', and converting underscores to spaces -engine => the L<Bio::Ontology::OntologyEngineI> object to be reused (will be created otherwise); note that every L<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;