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1 # $Id: goflat.pm,v 1.1.2.3 2003/05/27 22:00:52 lapp Exp $
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2 #
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3 # BioPerl module for Bio::OntologyIO::goflat
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4 #
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5 # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com>
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6 #
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7 # (c) Christian M. Zmasek, czmasek@gnf.org, 2002.
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8 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
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9 #
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10 # You may distribute this module under the same terms as perl itself.
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11 # Refer to the Perl Artistic License (see the license accompanying this
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12 # software package, or see http://www.perl.com/language/misc/Artistic.html)
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13 # for the terms under which you may use, modify, and redistribute this module.
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14 #
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15 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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16 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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17 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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18 #
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19 # You may distribute this module under the same terms as perl itself
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20
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21 # POD documentation - main docs before the code
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22
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23 =head1 NAME
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24
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25 goflat - a parser for the Gene Ontology flat-file format
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26
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27 =head1 SYNOPSIS
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28
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29 use Bio::OntologyIO;
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30
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31 # do not use directly -- use via Bio::OntologyIO
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32 my $parser = Bio::OntologyIO->new
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33 ( -format => "go",
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34 -defs_file => "/home/czmasek/GO/GO.defs",
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35 -files => ["/home/czmasek/GO/component.ontology",
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36 "/home/czmasek/GO/function.ontology",
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37 "/home/czmasek/GO/process.ontology"] );
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38
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39 my $go_ontology = $parser->next_ontology();
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40
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41 my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
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42 my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
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43
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44 =head1 DESCRIPTION
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45
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46 Needs Graph.pm from CPAN.
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47
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48 This is essentially a very thin derivation of the dagflat parser.
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49
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50 =head1 FEEDBACK
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51
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52 =head2 Mailing Lists
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53
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54 User feedback is an integral part of the evolution of this and other
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55 Bioperl modules. Send your comments and suggestions preferably to the
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56 Bioperl mailing lists Your participation is much appreciated.
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57
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58 bioperl-l@bioperl.org - General discussion
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59 http://bio.perl.org/MailList.html - About the mailing lists
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60
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61 =head2 Reporting Bugs
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62
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63 report bugs to the Bioperl bug tracking system to help us keep track
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64 the bugs and their resolution. Bug reports can be submitted via
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65 email or the web:
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66
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67 bioperl-bugs@bio.perl.org
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68 http://bugzilla.bioperl.org/
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69
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70 =head1 AUTHOR
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71
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72 Christian M. Zmasek
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73
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74 Email: czmasek@gnf.org or cmzmasek@yahoo.com
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75
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76 WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
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77
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78 Address:
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79
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80 Genomics Institute of the Novartis Research Foundation
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81 10675 John Jay Hopkins Drive
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82 San Diego, CA 92121
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83
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84 =head2 CONTRIBUTOR
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85
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86 Hilmar Lapp, hlapp at gmx.net
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87
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88 =head1 APPENDIX
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89
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90 The rest of the documentation details each of the object
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91 methods. Internal methods are usually preceded with a _
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92
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93 =cut
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94
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95
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96 # Let the code begin...
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97
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98
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99 package Bio::OntologyIO::goflat;
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100
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101 use vars qw( @ISA );
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102 use strict;
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103
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104 use Bio::Ontology::TermFactory;
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105 use Bio::OntologyIO::dagflat;
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106
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107 use constant TRUE => 1;
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108 use constant FALSE => 0;
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109
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110
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111 @ISA = qw( Bio::OntologyIO::dagflat );
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112
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113
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114 =head2 new
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115
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116 Title : new
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117 Usage : $parser = Bio::OntologyIO->new(
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118 -format => "go",
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119 -defs_file => "/path/to/GO.defs",
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120 -files => ["/path/to/component.ontology",
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121 "/path/to/function.ontology",
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122 "/path/to/process.ontology"] );
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123 Function: Creates a new goflat parser.
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124 Returns : A new goflat parser object, implementing L<Bio::OntologyIO>.
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125 Args : -defs_file => the name of the file holding the term
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126 definitions
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127 -files => a single ontology flat file holding the
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128 term relationships, or an array ref holding
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129 the file names (for GO, there will usually be
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130 3 files: component.ontology, function.ontology,
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131 process.ontology)
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132 -file => if there is only a single flat file, it may
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133 also be specified via the -file parameter
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134 -ontology_name => the name of the ontology; if not specified the
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135 parser will auto-discover it by using the term
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136 that starts with a '$', and converting underscores
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137 to spaces
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138 -engine => the Bio::Ontology::OntologyEngineI object
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139 to be reused (will be created otherwise); note
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140 that every Bio::Ontology::OntologyI will
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141 qualify as well since that one inherits from the
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142 former.
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143
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144 =cut
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145
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146 # in reality, we let OntologyIO::new do the instantiation, and override
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147 # _initialize for all initialization work
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148 sub _initialize {
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149 my ($self, @args) = @_;
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150
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151 $self->SUPER::_initialize( @args );
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152
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153 # default term object factory
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154 $self->term_factory(Bio::Ontology::TermFactory->new(
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155 -type => "Bio::Ontology::GOterm"))
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156 unless $self->term_factory();
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157
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158 } # _initialize
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159
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160
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161 1;
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