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