branch-1-6/Bio/OntologyIO/goflat.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::OntologyIO::goflat
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
   8 #
   9 # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
  10 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
  11 #
  12 # You may distribute this module under the same terms as perl itself.
  13 # Refer to the Perl Artistic License (see the license accompanying this
  14 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  15 # for the terms under which you may use, modify, and redistribute this module.
  16 #
  17 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  18 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  19 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  20 #
  21 # You may distribute this module under the same terms as perl itself
  22
  23 # POD documentation - main docs before the code
  24
  25 =head1 NAME
  26
  27 Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format
  28
  29 =head1 SYNOPSIS
  30
  31   use Bio::OntologyIO;
  32
  33   # do not use directly -- use via Bio::OntologyIO
  34   my $parser = Bio::OntologyIO->new
  35         ( -format       => "go",
  36      -defs_file    => "/home/czmasek/GO/GO.defs",
  37           -files        => ["/home/czmasek/GO/component.ontology",
  38                             "/home/czmasek/GO/function.ontology",
  39                             "/home/czmasek/GO/process.ontology"] );
  40
  41   my $go_ontology = $parser->next_ontology();
  42
  43   my $IS_A    = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
  44   my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
  45
  46 =head1 DESCRIPTION
  47
  48 Needs Graph.pm from CPAN.
  49
  50 This is essentially a very thin derivation of the dagflat parser.
  51
  52 =head1 FEEDBACK
  53
  54 =head2 Mailing Lists
  55
  56 User feedback is an integral part of the evolution of this and other
  57 Bioperl modules. Send your comments and suggestions preferably to the
  58 Bioperl mailing lists  Your participation is much appreciated.
  59
  60   bioperl-l@bioperl.org                  - General discussion
  61   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  62
  63 =head2 Support
  64
  65 Please direct usage questions or support issues to the mailing list:
  66
  67 I<bioperl-l@bioperl.org>
  68
  69 rather than to the module maintainer directly. Many experienced and
  70 reponsive experts will be able look at the problem and quickly
  71 address it. Please include a thorough description of the problem
  72 with code and data examples if at all possible.
  73
  74 =head2 Reporting Bugs
  75
  76 Report bugs to the Bioperl bug tracking system to help us keep track
  77 the bugs and their resolution.  Bug reports can be submitted via the
  78 web:
  79
  80   http://bugzilla.open-bio.org/
  81
  82 =head1 AUTHOR
  83
  84 Christian M. Zmasek
  85
  86 Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com
  87
  88 WWW:   http://monochrome-effect.net/
  89
  90 Address:
  91
  92   Genomics Institute of the Novartis Research Foundation
  93   10675 John Jay Hopkins Drive
  94   San Diego, CA 92121
  95
  96 =head2 CONTRIBUTOR
  97
  98  Hilmar Lapp, hlapp at gmx.net
  99
 100 =head1 APPENDIX
 101
 102 The rest of the documentation details each of the object
 103 methods. Internal methods are usually preceded with a _
 104
 105 =cut
 106
 107
 108 # Let the code begin...
 109
 110
 111 package  Bio::OntologyIO::goflat;
 112
 113 use strict;
 114
 115 use Bio::Ontology::TermFactory;
 116
 117 use constant TRUE         => 1;
 118 use constant FALSE        => 0;
 119
 120
 121 use base qw(Bio::OntologyIO::dagflat);
 122
 123
 124 =head2 new
 125
 126  Title   : new
 127  Usage   : $parser = Bio::OntologyIO->new(
 128                              -format => "go",
 129                              -defs_file => "/path/to/GO.defs",
 130                              -files => ["/path/to/component.ontology",
 131                                         "/path/to/function.ontology",
 132                                         "/path/to/process.ontology"] );
 133  Function: Creates a new goflat parser.
 134  Returns : A new goflat parser object, implementing Bio::OntologyIO.
 135  Args    : -defs_file  => the name of the file holding the term
 136                           definitions
 137            -files      => a single ontology flat file holding the
 138                           term relationships, or an array ref holding
 139                           the file names (for GO, there will usually be
 140                           3 files: component.ontology, function.ontology,
 141                           process.ontology)
 142            -file       => if there is only a single flat file, it may
 143                           also be specified via the -file parameter
 144            -ontology_name => the name of the ontology; if not specified the
 145                           parser will auto-discover it by using the term
 146                           that starts with a $, and converting underscores
 147                           to spaces
 148            -engine     => the Bio::Ontology::OntologyEngineI object
 149                           to be reused (will be created otherwise); note
 150                           that every Bio::Ontology::OntologyI will
 151                           qualify as well since that one inherits from the
 152                           former.
 153
 154 See L<Bio::OntologyIO>.
 155
 156 =cut
 157
 158 # in reality, we let OntologyIO::new do the instantiation, and override
 159 # _initialize for all initialization work
 160 sub _initialize {
 161     my ($self, @args) = @_;
 162
 163     $self->SUPER::_initialize( @args );
 164
 165     # default term object factory
 166     $self->term_factory(Bio::Ontology::TermFactory->new(
 167                                           -type => "Bio::Ontology::GOterm"))
 168         unless $self->term_factory();
 169
 170 } # _initialize
 171
 172
 173 1;