Bio/Ontology/SimpleGOEngine.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Ontology::SimpleGOEngine
   4 #
   5 # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com>
   6 #
   7 # (c) Christian M. Zmasek, czmasek@gnf.org, 2002.
   8 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
   9 #
  10 # You may distribute this module under the same terms as perl itself.
  11 # Refer to the Perl Artistic License (see the license accompanying this
  12 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  13 # for the terms under which you may use, modify, and redistribute this module.
  14 #
  15 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  16 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  17 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  18 #
  19 # You may distribute this module under the same terms as perl itself
  20
  21 # POD documentation - main docs before the code
  22
  23 =head1 NAME
  24
  25 Bio::Ontology::SimpleGOEngine - a Ontology Engine for GO implementing OntologyEngineI
  26
  27 =head1 SYNOPSIS
  28
  29   use Bio::Ontology::SimpleGOEngine;
  30
  31   my $parser = Bio::Ontology::SimpleGOEngine->new
  32         ( -defs_file => "/home/czmasek/GO/GO.defs",
  33           -files     => ["/home/czmasek/GO/component.ontology",
  34                          "/home/czmasek/GO/function.ontology",
  35                          "/home/czmasek/GO/process.ontology"] );
  36
  37   my $engine = $parser->parse();
  38
  39   my $IS_A       = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
  40   my $PART_OF    = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
  41   my $RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );
  42
  43 =head1 DESCRIPTION
  44
  45 This class is deprecated and instead Bio::Ontology::OBOEngine should be used.
  46
  47 Needs Graph.pm from CPAN.
  48
  49 =head1 FEEDBACK
  50
  51 =head2 Mailing Lists
  52
  53 User feedback is an integral part of the evolution of this and other
  54 Bioperl modules. Send your comments and suggestions preferably to the
  55 Bioperl mailing lists  Your participation is much appreciated.
  56
  57   bioperl-l@bioperl.org                  - General discussion
  58   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  59
  60 =head2 Reporting Bugs
  61
  62 Report bugs to the Bioperl bug tracking system to help us keep track
  63 the bugs and their resolution.  Bug reports can be submitted via
  64 the web:
  65
  66   http://bugzilla.open-bio.org/
  67
  68 =head1 AUTHOR
  69
  70 Christian M. Zmasek
  71
  72 Email: czmasek@gnf.org  or  cmzmasek@yahoo.com
  73
  74 WWW:   http://www.genetics.wustl.edu/eddy/people/zmasek/
  75
  76 Address:
  77
  78   Genomics Institute of the Novartis Research Foundation
  79   10675 John Jay Hopkins Drive
  80   San Diego, CA 92121
  81
  82 =head1 APPENDIX
  83
  84 The rest of the documentation details each of the object
  85 methods. Internal methods are usually preceded with a _
  86
  87 =cut
  88
  89
  90 # Let the code begin...
  91 package Bio::Ontology::SimpleGOEngine;
  92
  93 use strict;
  94
  95 use base qw(Bio::Ontology::OBOEngine);
  96
  97
  98 # Internal methods
  99 # ----------------
 100
 101 ## Overiding this method from OBOEngine
 102 # Checks the correct format of a GOBO-formatted id
 103 # Gets the id out of a term or id string
 104 sub _get_id {
 105     my ( $self, $term ) = @_;
 106     my $id = $term;
 107
 108     if(ref($term)) {
 109         # use TermI standard API
 110         $self->throw("Object doesn't implement Bio::Ontology::TermI. ".
 111                      "Bummer.")
 112             unless $term->isa("Bio::Ontology::TermI");
 113         $id = $term->identifier();
 114         # if there is no ID, we need to fake one from ontology name and name
 115         # in order to achieve uniqueness
 116         if(!$id) {
 117             $id = $term->ontology->name() if $term->ontology();
 118             $id = $id ? $id.'|' : '';
 119             $id .= $term->name();
 120         }
 121     }
 122     # don't fuss if it looks remotely standard, and we trust GO terms
 123     return $id
 124 #        if $term->isa("Bio::Ontology::GOterm")||($id =~ /^[A-Z_]{1,8}:\d{1,}$/);
 125         if $term->isa("Bio::Ontology::GOterm")||($id =~ /^\w+:\w+$/);
 126     # prefix with something if only numbers
 127     if($id =~ /^\d+$/) {
 128         $self->warn(ref($self).": identifier [$id] is only numbers - ".
 129                     "prefixing with 'GO:'");
 130         return "GO:" . $id;
 131     }
 132     # we shouldn't have gotten here if it's at least a remotely decent ID
 133     $self->throw(ref($self).": non-standard identifier '$id'\n")
 134         unless $id =~ /\|/;
 135     return $id;
 136 } # _get_id
 137
 138
 139 1;