lib/Bio/OntologyIO/soflat.pm

   1 #
   2 # BioPerl module for Bio::OntologyIO::soflat
   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) Hilmar Lapp, hlapp at gnf.org, 2003.
  10 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002-3.
  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::soflat - a parser for the Sequence 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       => "so", # or soflat
  36      -defs_file    => "/home/czmasek/SO/SO.defs",
  37           -file         => "/home/czmasek/SO/sofa.ontology" );
  38
  39   my $sofa_ontology = $parser->next_ontology();
  40
  41   my $IS_A    = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
  42   my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
  43
  44 =head1 DESCRIPTION
  45
  46 Needs Graph.pm from CPAN.
  47
  48 This is essentially a very thin derivation of the dagflat base-parser.
  49
  50 =head1 FEEDBACK
  51
  52 =head2 Mailing Lists
  53
  54 User feedback is an integral part of the evolution of this and other
  55 Bioperl modules. Send your comments and suggestions preferably to the
  56 Bioperl mailing lists  Your participation is much appreciated.
  57
  58   bioperl-l@bioperl.org                  - General discussion
  59   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  60
  61 =head2 Support
  62
  63 Please direct usage questions or support issues to the mailing list:
  64
  65 I<bioperl-l@bioperl.org>
  66
  67 rather than to the module maintainer directly. Many experienced and
  68 reponsive experts will be able look at the problem and quickly
  69 address it. Please include a thorough description of the problem
  70 with code and data examples if at all possible.
  71
  72 =head2 Reporting Bugs
  73
  74 Report bugs to the Bioperl bug tracking system to help us keep track
  75 the bugs and their resolution.  Bug reports can be submitted via the
  76 web:
  77
  78   https://github.com/bioperl/bioperl-live/issues
  79
  80 =head1 AUTHOR
  81
  82 Christian M. Zmasek
  83
  84 Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com
  85
  86 WWW:   http://monochrome-effect.net/
  87
  88 Address:
  89
  90   Genomics Institute of the Novartis Research Foundation
  91   10675 John Jay Hopkins Drive
  92   San Diego, CA 92121
  93
  94 =head2 CONTRIBUTOR
  95
  96  Hilmar Lapp, hlapp at gmx.net
  97
  98 =head1 APPENDIX
  99
 100 The rest of the documentation details each of the object
 101 methods. Internal methods are usually preceded with a _
 102
 103 =cut
 104
 105
 106 # Let the code begin...
 107
 108
 109 package  Bio::OntologyIO::soflat;
 110
 111 use strict;
 112
 113 use Bio::Ontology::TermFactory;
 114
 115 use constant TRUE         => 1;
 116 use constant FALSE        => 0;
 117
 118
 119 use base qw(Bio::OntologyIO::dagflat);
 120
 121
 122 =head2 new
 123
 124  Title   : new
 125  Usage   : $parser = Bio::OntologyIO->new(
 126                              -format => "soflat",
 127                              -files => ["/path/to/sofa.ontology"] );
 128  Function: Creates a new soflat parser.
 129  Returns : A new soflat parser object, implementing Bio::OntologyIO.
 130  Args    : -defs_file  => the name of the file holding the term
 131                           definitions
 132            -files      => a single ontology flat file holding the
 133                           term relationships, or an array ref holding
 134                           the file names
 135            -file       => if there is only a single flat file, it may
 136                           also be specified via the -file parameter
 137            -ontology_name => the name of the ontology; if not specified the
 138                           parser will auto-discover it by using the term
 139                           that starts with a $, and converting underscores
 140                           to spaces
 141            -engine     => the Bio::Ontology::OntologyEngineI object
 142                           to be reused (will be created otherwise); note
 143                           that every Bio::Ontology::OntologyI will
 144                           qualify as well since that one inherits from the
 145                           former.
 146
 147 See L<Bio::Ontology::OntologyI>.
 148
 149 =cut
 150
 151 # in reality, we let OntologyIO::new do the instantiation, and override
 152 # _initialize for all initialization work
 153 sub _initialize {
 154     my ($self, @args) = @_;
 155
 156     $self->SUPER::_initialize( @args );
 157
 158     # default term object factory
 159     $self->term_factory(Bio::Ontology::TermFactory->new(
 160                                           -type => "Bio::Ontology::GOterm"))
 161         unless $self->term_factory();
 162
 163 } # _initialize
 164
 165
 166 1;