Bio/OntologyIO/soflat.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::OntologyIO::soflat
   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) Hilmar Lapp, hlapp at gnf.org, 2003.
   9 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002-3.
  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::soflat - a parser for the Sequence 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       => "so", # or soflat
  35      -defs_file    => "/home/czmasek/SO/SO.defs",
  36           -file         => "/home/czmasek/SO/sofa.ontology" );
  37
  38   my $sofa_ontology = $parser->next_ontology();
  39
  40   my $IS_A    = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
  41   my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
  42
  43 =head1 DESCRIPTION
  44
  45 Needs Graph.pm from CPAN.
  46
  47 This is essentially a very thin derivation of the dagflat base-parser.
  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 the
  64 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 =head2 CONTRIBUTOR
  83
  84  Hilmar Lapp, hlapp at gmx.net
  85
  86 =head1 APPENDIX
  87
  88 The rest of the documentation details each of the object
  89 methods. Internal methods are usually preceded with a _
  90
  91 =cut
  92
  93
  94 # Let the code begin...
  95
  96
  97 package  Bio::OntologyIO::soflat;
  98
  99 use strict;
 100
 101 use Bio::Ontology::TermFactory;
 102
 103 use constant TRUE         => 1;
 104 use constant FALSE        => 0;
 105
 106
 107 use base qw(Bio::OntologyIO::dagflat);
 108
 109
 110 =head2 new
 111
 112  Title   : new
 113  Usage   : $parser = Bio::OntologyIO->new(
 114                              -format => "soflat",
 115                              -files => ["/path/to/sofa.ontology"] );
 116  Function: Creates a new soflat parser.
 117  Returns : A new soflat parser object, implementing Bio::OntologyIO.
 118  Args    : -defs_file  => the name of the file holding the term
 119                           definitions
 120            -files      => a single ontology flat file holding the
 121                           term relationships, or an array ref holding
 122                           the file names
 123            -file       => if there is only a single flat file, it may
 124                           also be specified via the -file parameter
 125            -ontology_name => the name of the ontology; if not specified the
 126                           parser will auto-discover it by using the term
 127                           that starts with a $, and converting underscores
 128                           to spaces
 129            -engine     => the Bio::Ontology::OntologyEngineI object
 130                           to be reused (will be created otherwise); note
 131                           that every Bio::Ontology::OntologyI will
 132                           qualify as well since that one inherits from the
 133                           former.
 134
 135 See L<Bio::Ontology::OntologyI>.
 136
 137 =cut
 138
 139 # in reality, we let OntologyIO::new do the instantiation, and override
 140 # _initialize for all initialization work
 141 sub _initialize {
 142     my ($self, @args) = @_;
 143
 144     $self->SUPER::_initialize( @args );
 145
 146     # default term object factory
 147     $self->term_factory(Bio::Ontology::TermFactory->new(
 148                                           -type => "Bio::Ontology::GOterm"))
 149         unless $self->term_factory();
 150
 151 } # _initialize
 152
 153
 154 1;