Raw content of Bio::OntologyIO # $Id: OntologyIO.pm,v 2003/03/13 02:09:19 lapp Exp $ # # BioPerl module for Bio::OntologyIO # # Cared for by Hilmar Lapp <hlapp at gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # 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. # # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO - Parser factory for Ontology formats =head1 SYNOPSIS use Bio::OntologyIO; my $parser = Bio::OntologyIO->new(-format => "go", ...); while(my $ont = $parser->next_ontology()) { print "read ontology ",$ont->name()," with ", scalar($ont->get_root_terms)," root terms, and ", scalar($ont->get_leaf_terms)," leaf terms\n"; } =head1 DESCRIPTION This is the parser factory for different ontology sources and formats. Conceptually, it is very similar to L<Bio::SeqIO>, but the difference is that the chunk of data returned as an object is an entire ontology. =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 list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =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; use vars qw(@ISA); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use Bio::Root::IO; @ISA = qw(Bio::Root::Root Bio::Root::IO); # # Maps from format name to driver suitable for the format. # my %format_driver_map = ( "go" => "goflat", "so" => "soflat", "interpro" => "InterProParser", ); =head2 new Title : new Usage : my $parser = Bio::OntologyIO->new(-format => 'go', @args); Function: Returns a stream of ontologies opened on the specified input for the specified format. Returns : An ontology parser (an instance of Bio::OntologyIO) initialized for the specified format. Args : Named parameters. Common parameters are -format - the format of the input; supported right now are 'go' (synonymous with goflat), 'so' (synonymous with soflat), and 'interpro' -file - the file holding the data -fh - the stream providing the data (-file and -fh are mutually exclusive) -ontology_name - the name of the ontology -engine - the L<Bio::Ontology::OntologyEngineI> object to be reused (will be created otherwise); note that every L<Bio::Ontology::OntologyI> will qualify as well since that one inherits from the former. -term_factory - the ontology term factory to use. Provide a value only if you know what you are doing. DAG-Edit flat file parsers will usually also accept the following parameters. -defs_file - the name of the file holding the term definitions -files - an array ref holding the file names (for GO, there will usually be 3 files: component.ontology, function.ontology, process.ontology) Other parameters are specific to the parsers. =cut sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::OntologyIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $class->_map_format($param{'-format'}); # normalize capitalization return undef unless( $class->_load_format_module($format) ); return "Bio::OntologyIO::$format"->new(@args); } } sub _initialize { my($self, @args) = @_; # initialize factories etc my ($eng,$fact,$ontname) = $self->_rearrange([qw(TERM_FACTORY) ], @args); # term object factory $self->term_factory($fact) if $fact; # initialize the Bio::Root::IO part $self->_initialize_io(@args); } =head2 next_ontology Title : next_ontology Usage : $ont = $stream->next_ontology() Function: Reads the next ontology object from the stream and returns it. Returns : a L<Bio::Ontology::OntologyI> compliant object, or undef at the end of the stream Args : none =cut sub next_ontology { shift->throw_not_implemented(); } =head2 term_factory Title : term_factory Usage : $obj->term_factory($newval) Function: Get/set the ontology term factory to use. As a user of this module it is not necessary to call this method as there will be default. In order to change the default, the easiest way is to instantiate L<Bio::Ontology::TermFactory> with the proper -type argument. Most if not all parsers will actually use this very implementation, so even easier than the aforementioned way is to simply call $ontio->term_factory->type("Bio::Ontology::MyTerm"). Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI object) Args : on set, new value (a Bio::Factory::ObjectFactoryI object, optional) =cut sub term_factory{ my $self = shift; return $self->{'term_factory'} = shift if @_; return $self->{'term_factory'}; } =head1 Private Methods Some of these are actually 'protected' in OO speak, which means you may or will want to utilize them in a derived ontology parser, but you should not call them from outside. =cut =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL OntologyIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self, $format) = @_; my $module = "Bio::OntologyIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <<END; $self: $format cannot be found Exception $@ For more information about the OntologyIO system please see the docs. This includes ways of checking for formats at compile time, not run time END } return $ok; } sub DESTROY { my $self = shift; $self->close(); } sub _map_format { my $self = shift; my $format = shift; my $mod; if($format) { $mod = $format_driver_map{lc($format)}; $mod = lc($format) unless $mod; } else { $self->throw("unable to guess ontology format, specify -format"); } return $mod; } 1;