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1 # $Id: SimilarityPair.pm,v 1.21 2002/12/24 15:15:32 jason Exp $
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2 #
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3 # BioPerl module for Bio::SeqFeature::SimilarityPair
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4 #
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5 # Cared for by Hilmar Lapp <hlapp@gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
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16 of two sequences.
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17
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18 =head1 SYNOPSIS
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19
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20 $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit);
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21
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22 $sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object - the query
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23 $sim = $sim_pair->hit(); # dto - the hit.
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24
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25 # some properties for the similarity pair
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26 $expect = $sim_pair->significance();
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27 $score = $sim_pair->score();
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28 $bitscore = $sim_pair->bits();
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29
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30 # this will not write the description for the sequence (only its name)
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31 print $sim_pair->query()->gff_string(), "\n";
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32
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33 =head1 DESCRIPTION
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34
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35 Lightweight similarity search result as a pair of Similarity
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36 features. This class inherits off Bio::SeqFeature::FeaturePair and
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37 therefore implements Bio::SeqFeatureI, whereas the two features of the
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38 pair are descendants of Bio::SeqFeature::Generic, with better support
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39 for representing similarity search results in a cleaner way.
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40
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41 =head1 FEEDBACK
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42
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43 =head2 Mailing Lists
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44
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45 User feedback is an integral part of the evolution of this and other
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46 Bioperl modules. Send your comments and suggestions preferably to one
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47 of the Bioperl mailing lists. Your participation is much appreciated.
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48
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49 bioperl-l@bioperl.org - General discussion
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50 http://bio.perl.org/MailList.html - About the mailing lists
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51
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52 =head2 Reporting Bugs
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53
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54 Report bugs to the Bioperl bug tracking system to help us keep track
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55 the bugs and their resolution. Bug reports can be submitted via
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56 email or the web:
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57
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58 bioperl-bugs@bio.perl.org
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59 http://bugzilla.bioperl.org/
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60
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61 =head1 AUTHOR - Hilmar Lapp
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62
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63 Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
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64
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65 Describe contact details here
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66
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67 =head1 APPENDIX
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68
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69 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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70
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71 =cut
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72
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73
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74 # Let the code begin...
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75
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76
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77 package Bio::SeqFeature::SimilarityPair;
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78 use vars qw(@ISA);
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79 use strict;
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80
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81 use Bio::SeqFeature::FeaturePair;
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82 use Bio::SeqFeature::Similarity;
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83 use Bio::SearchIO;
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84
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85 @ISA = qw(Bio::SeqFeature::FeaturePair);
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86
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87 =head2 new
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88
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89 Title : new
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90 Usage : my $similarityPair = new Bio::SeqFeature::SimilarityPair
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91 (-hit => $hit,
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92 -query => $query,
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93 -source => 'blastp');
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94 Function: Initializes a new SimilarityPair object
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95 Returns : Bio::SeqFeature::SimilarityPair
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96 Args : -query => The query in a Feature pair
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97 -hit => (formerly '-subject') the subject/hit in a Feature pair
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98
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99
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100 =cut
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101
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102 sub new {
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103 my($class,@args) = @_;
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104
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105 my $self = $class->SUPER::new(@args);
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106
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107 # Hack to deal with the fact that SimilarityPair calls strand()
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108 # which will lead to an error in Bio::Search::HSP::BlastHSP
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109 # because parsing hasn't yet occurred.
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110 # TODO: Remove this when BlastHSP doesn't do lazy parsing.
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111 $self->{'_initializing'} = 1;
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112
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113 my ($primary, $hit, $query, $fea1, $source,$sbjct) =
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114 $self->_rearrange([qw(PRIMARY
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115 HIT
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116 QUERY
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117 FEATURE1
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118 SOURCE
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119 SUBJECT
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120 )],@args);
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121
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122 if( $sbjct ) {
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123 # undeprecated by Jason before 1.1 release
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124 # $self->deprecated("use of -subject deprecated: SimilarityPair now uses 'hit'");
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125 if(! $hit) { $hit = $sbjct }
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126 else {
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127 $self->warn("-hit and -subject were specified, using -hit and ignoring -subject");
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128 }
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129 }
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130
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131 # make sure at least the query feature exists -- this refers to feature1
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132 if($query && ! $fea1) { $self->query( $query); }
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133 else { $self->query('null'); } # call with no args sets a default value for query
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134
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135 $hit && $self->hit($hit);
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136 # the following refer to feature1, which has been ensured to exist
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137 if( defined $primary || ! defined $self->primary_tag) {
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138 $primary = 'similarity' unless defined $primary;
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139 $self->primary_tag($primary);
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140 }
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141
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142 $source && $self->source_tag($source);
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143 $self->strand(0) unless( defined $self->strand() );
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144
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145 $self->{'_initializing'} = 0; # See "Hack" note above
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146 return $self;
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147 }
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148
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149 #
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150 # Everything else is just inherited from SeqFeature::FeaturePair.
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151 #
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152
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153 =head2 query
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154
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155 Title : query
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156 Usage : $query_feature = $obj->query();
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157 $obj->query($query_feature);
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158 Function: The query object for this similarity pair
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159 Returns : Bio::SeqFeature::Similarity
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160 Args : [optional] Bio::SeqFeature::Similarity
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161
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162 See L<Bio::SeqFeature::Similarity>, L<Bio::SeqFeature::FeaturePair>
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163
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164 =cut
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165
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166 sub query {
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167 my ($self, @args) = @_;
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168 my $f = $self->feature1();
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169 if( ! @args || ( !ref($args[0]) && $args[0] eq 'null') ) {
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170 if( ! defined( $f) ) {
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171 @args = Bio::SeqFeature::Similarity->new();
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172 } elsif( ! $f->isa('Bio::SeqFeature::Similarity') &&
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173 $f->isa('Bio::SeqFeatureI') ) {
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174 # a Bio::SeqFeature::Generic was placeholder for feature1
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175 my $newf = new
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176 Bio::SeqFeature::Similarity( -start => $f->start(),
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177 -end => $f->end(),
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178 -strand => $f->strand(),
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179 -primary => $f->primary_tag(),
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180 -source => $f->source_tag(),
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181 -seq_id => $f->seq_id(),
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182 -score => $f->score(),
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183 -frame => $f->frame(),
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184 );
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185 foreach my $tag ( $newf->all_tags ) {
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186 $tag->add_tag($tag, $newf->each_tag($tag));
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187 }
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188 @args = $newf;
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189 } else {
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190 @args = ();
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191 }
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192 }
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193 return $self->feature1(@args);
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194 }
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195
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196
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197
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198
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199 =head2 subject
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200
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201 Title : subject
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202 Usage : $sbjct_feature = $obj->subject();
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203 $obj->subject($sbjct_feature);
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204 Function: Get/Set Subject for a SimilarityPair
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205 Returns : Bio::SeqFeature::Similarity
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206 Args : [optional] Bio::SeqFeature::Similarity
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207 Notes : Deprecated. Use the method 'hit' instead
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208
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209 =cut
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210
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211 sub subject {
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212 my $self = shift;
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213 # $self->deprecated("Method subject deprecated: use hit() instead");
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214 $self->hit(@_);
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215 }
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216
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217 *sbjct = \&subject;
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218
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219 =head2 hit
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220
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221 Title : hit
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222 Usage : $sbjct_feature = $obj->hit();
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223 $obj->hit($sbjct_feature);
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224 Function: Get/Set Hit for a SimilarityPair
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225 Returns : Bio::SeqFeature::Similarity
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226 Args : [optional] Bio::SeqFeature::Similarity
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227
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228
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229 =cut
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230
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231 sub hit {
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232 my ($self, @args) = @_;
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233 my $f = $self->feature2();
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234 if(! @args || (!ref($args[0]) && $args[0] eq 'null') ) {
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235 if( ! defined( $f) ) {
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236 @args = Bio::SeqFeature::Similarity->new();
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237 } elsif( ! $f->isa('Bio::SeqFeature::Similarity') &&
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238 $f->isa('Bio::SeqFeatureI')) {
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239 # a Bio::SeqFeature::Generic was placeholder for feature2
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240 my $newf = new
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241 Bio::SeqFeature::Similarity( -start => $f->start(),
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242 -end => $f->end(),
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243 -strand => $f->strand(),
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244 -primary => $f->primary_tag(),
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245 -source => $f->source_tag(),
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246 -seq_id => $f->seq_id(),
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247 -score => $f->score(),
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248 -frame => $f->frame(),
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249 );
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250 foreach my $tag ( $newf->all_tags ) {
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251 $tag->add_tag($tag, $newf->each_tag($tag));
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252 }
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253 @args = $newf;
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254 }
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255 }
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256 return $self->feature2(@args);
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257 }
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258
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259 =head2 source_tag
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260
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261 Title : source_tag
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262 Usage : $source = $obj->source_tag(); # i.e., program
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263 $obj->source_tag($evalue);
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264 Function: Gets the source tag (program name typically) for a feature
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265 Returns : string
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266 Args : [optional] string
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267
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268
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269 =cut
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270
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271 sub source_tag {
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272 my ($self, @args) = @_;
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273
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274 if(@args) {
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275 $self->hit()->source_tag(@args);
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276 }
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277 return $self->query()->source_tag(@args);
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278 }
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279
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280 =head2 significance
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281
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282 Title : significance
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283 Usage : $evalue = $obj->significance();
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284 $obj->significance($evalue);
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285 Function:
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286 Returns :
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287 Args :
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288
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289
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290 =cut
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291
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292 sub significance {
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293 my ($self, @args) = @_;
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294
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295 if(@args) {
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296 $self->hit()->significance(@args);
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297 }
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298 return $self->query()->significance(@args);
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299 }
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300
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301 =head2 score
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302
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303 Title : score
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304 Usage : $score = $obj->score();
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305 $obj->score($value);
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306 Function:
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307 Returns :
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308 Args :
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309
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310
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311 =cut
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312
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313 sub score {
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314 my ($self, @args) = @_;
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315
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316 if(@args) {
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317 $self->hit()->score(@args);
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318 }
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319 return $self->query()->score(@args);
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320 }
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321
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322 =head2 bits
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323
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324 Title : bits
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325 Usage : $bits = $obj->bits();
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326 $obj->bits($value);
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327 Function:
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328 Returns :
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329 Args :
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330
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331
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332 =cut
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333
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334 sub bits {
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335 my ($self, @args) = @_;
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336
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337 if(@args) {
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338 $self->hit()->bits(@args);
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339 }
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340 return $self->query()->bits(@args);
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341 }
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342
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343 1;
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