Bio/OntologyIO/goflat.pm

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