Bio/OntologyIO/soflat.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::OntologyIO::soflat
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com>
   8 #
   9 # (c) Christian M. Zmasek, czmasek@gnf.org, 2002.
  10 # (c) Hilmar Lapp, hlapp at gnf.org, 2003.
  11 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002-3.
  12 #
  13 # You may distribute this module under the same terms as perl itself.
  14 # Refer to the Perl Artistic License (see the license accompanying this
  15 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  16 # for the terms under which you may use, modify, and redistribute this module.
  17 #
  18 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  19 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  20 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  21 #
  22 # You may distribute this module under the same terms as perl itself
  23
  24 # POD documentation - main docs before the code
  25
  26 =head1 NAME
  27
  28 Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format
  29
  30 =head1 SYNOPSIS
  31
  32   use Bio::OntologyIO;
  33
  34   # do not use directly -- use via Bio::OntologyIO
  35   my $parser = Bio::OntologyIO->new
  36         ( -format       => "so", # or soflat
  37      -defs_file    => "/home/czmasek/SO/SO.defs",
  38           -file         => "/home/czmasek/SO/sofa.ontology" );
  39
  40   my $sofa_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 base-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 L<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   http://bugzilla.open-bio.org/
  80
  81 =head1 AUTHOR
  82
  83 Christian M. Zmasek
  84
  85 Email: czmasek@gnf.org  or  cmzmasek@yahoo.com
  86
  87 WWW:   http://www.genetics.wustl.edu/eddy/people/zmasek/
  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::soflat;
 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 => "soflat",
 128                              -files => ["/path/to/sofa.ontology"] );
 129  Function: Creates a new soflat parser.
 130  Returns : A new soflat parser object, implementing Bio::OntologyIO.
 131  Args    : -defs_file  => the name of the file holding the term
 132                           definitions
 133            -files      => a single ontology flat file holding the
 134                           term relationships, or an array ref holding
 135                           the file names
 136            -file       => if there is only a single flat file, it may
 137                           also be specified via the -file parameter
 138            -ontology_name => the name of the ontology; if not specified the
 139                           parser will auto-discover it by using the term
 140                           that starts with a $, and converting underscores
 141                           to spaces
 142            -engine     => the Bio::Ontology::OntologyEngineI object
 143                           to be reused (will be created otherwise); note
 144                           that every Bio::Ontology::OntologyI will
 145                           qualify as well since that one inherits from the
 146                           former.
 147
 148 See L<Bio::Ontology::OntologyI>.
 149
 150 =cut
 151
 152 # in reality, we let OntologyIO::new do the instantiation, and override
 153 # _initialize for all initialization work
 154 sub _initialize {
 155     my ($self, @args) = @_;
 156
 157     $self->SUPER::_initialize( @args );
 158
 159     # default term object factory
 160     $self->term_factory(Bio::Ontology::TermFactory->new(
 161                                           -type => "Bio::Ontology::GOterm"))
 162         unless $self->term_factory();
 163
 164 } # _initialize
 165
 166
 167 1;