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2 #
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3 # BioPerl module for Bio::Tools::Sim4::Exon
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4 #
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5 # Cared for by Ewan Birney <birney@sanger.ac.uk>
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6 # and Hilmar Lapp <hlapp@gmx.net>
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7 #
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8 # Copyright Ewan Birney, Hilmar Lapp
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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
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12 # POD documentation - main docs before the code
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13
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14 =head1 NAME
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15
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16 Bio::Tools::Sim4::Exon - A single exon determined by an alignment
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17
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18 =head1 SYNOPSIS
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19
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20 # See Bio::Tools::Sim4::Results for a description of the context.
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21
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22 # an instance of this class is-a Bio::SeqFeature::SimilarityPair
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23
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24 # coordinates of the exon (recommended way):
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25 print "exon from ", $exon->start(),
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26 " to ", $exon->end(), "\n";
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27
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28 # the same (feature1() inherited from Bio::SeqFeature::FeaturePair)
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29 print "exon from ", $exon->feature1()->start(),
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30 " to ", $exon->feature1()->end(), "\n";
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31 # also the same (query() inherited from Bio::SeqFeature::SimilarityPair):
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32 print "exon from ", $exon->query()->start(),
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33 " to ", $exon->query()->end(), "\n";
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34
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35 # coordinates on the matching EST (recommended way):
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36 print "matches on EST from ", $exon->est_hit()->start(),
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37 " to ", $exon->est_hit()->end(), "\n";
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38
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39 # the same (feature2() inherited from Bio::SeqFeature::FeaturePair)
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40 print "matches on EST from ", $exon->feature2()->start(),
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41 " to ", $exon->feature2()->end(), "\n";
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42 # also the same (subject() inherited from Bio::SeqFeature::SimilarityPair):
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43 print "exon from ", $exon->subject()->start(),
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44 " to ", $exon->subject()->end(), "\n";
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45
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46 =head1 DESCRIPTION
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47
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48 This class inherits from Bio::SeqFeature::SimilarityPair and represents an
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49 exon on a genomic sequence determined by similarity, that is, by aligning an
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50 EST sequence (using Sim4 in this case). Consequently, the notion of query and
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51 subject is always from the perspective of the genomic sequence: query refers
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52 to the genomic seq, subject to the aligned EST hit. Because of this,
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53 $exon-E<gt>start(), $exon-E<gt>end() etc will always return what you expect.
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54
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55 To get the coordinates on the matching EST, refer to the properties of the
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56 feature returned by L<est_hit>().
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57
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58 =head1 FEEDBACK
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59
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60 =head2 Mailing Lists
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61
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62 User feedback is an integral part of the evolution of this
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63 and other Bioperl modules. Send your comments and suggestions preferably
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64 to one of the Bioperl mailing lists.
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65 Your participation is much appreciated.
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66
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67 bioperl-l@bioperl.org - General discussion
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68 http://bio.perl.org/MailList.html - About the mailing lists
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69
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70 =head2 Reporting Bugs
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71
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72 Report bugs to the Bioperl bug tracking system to help us keep track
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73 the bugs and their resolution.
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74 Bug reports can be submitted via email or the web:
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75
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76 bioperl-bugs@bio.perl.org
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77 http://bugzilla.bioperl.org/
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78
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79 =head1 AUTHOR - Ewan Birney, Hilmar Lapp
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80
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81 Email birney@sanger.ac.uk
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82 Hilmar Lapp E<lt>hlapp@gmx.netE<gt> or E<lt>hilmar.lapp@pharma.novartis.comE<gt>.
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83
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84 Describe contact details here
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85
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86 =head1 APPENDIX
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87
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88 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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89
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90 =cut
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91
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92
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93 # Let the code begin...
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94
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95
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96 package Bio::Tools::Sim4::Exon;
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97 use vars qw(@ISA);
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98 use strict;
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99
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100 use Bio::SeqFeature::FeaturePair;
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101 use Bio::SeqFeature::Generic;
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102 use Bio::SeqFeature::SimilarityPair;
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103
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104 @ISA = qw(Bio::SeqFeature::SimilarityPair);
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105
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106 sub new {
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107 my ($class,@args) = @_;
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108 my %param = @args;
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109 my $self = $class->SUPER::new(@args);
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110
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111 my ($prim, $source) = $self->_rearrange([qw(PRIMARY SOURCE)], @args);
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112
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113 $self->primary_tag('exon') unless $prim;
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114 $self->source_tag('Sim4') unless $source;
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115 $self->strand(0) unless defined($self->strand());
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116 $self->query();
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117 return $self;
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118 }
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119
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120 =head2 percentage_id
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121
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122 Title : percentage_id
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123 Usage : $obj->percentage_id($newval)
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124 Function: This is a synonym for 100 * $obj->est_hit()->frac_identical().
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125 Returns : value of percentage_id
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126 Args : newvalue (optional)
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127
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128
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129 =cut
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130
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131 sub percentage_id {
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132 my ($self, @args) = @_;
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133 my $frac;
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134 my $val;
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135 my $delegated = 0;
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136
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137 if(@args) {
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138 $frac = $args[0];
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139 $frac /= 100.0 if defined($frac);
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140 }
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141 if($self->query()->can('frac_identical')) {
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142 if(defined($frac)) {
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143 $self->query()->frac_identical($frac);
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144 }
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145 $val = 100.0 * $self->query()->frac_identical();
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146 $delegated = 1;
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147 }
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148 if($self->est_hit()->can('frac_identical')) {
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149 if(defined($frac)) {
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150 $self->est_hit()->frac_identical($frac);
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151 }
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152 # this intentiously overwrites previous $val
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153 $val = 100.0 * $self->est_hit()->frac_identical();
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154 $delegated = 1;
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155 }
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156 if(! $delegated) {
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157 if(@args) {
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158 $val = shift(@args);
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159 $self->{'percentage_id'} = $val;
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160 } else {
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161 $val = $self->{'percentage_id'};
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162 }
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163 }
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164 return $val;
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165 }
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166
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167 =head2 est_hit
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168
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169 Title : est_hit
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170 Usage : $est_feature = $obj->est_hit();
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171 Function: Returns the EST hit pointing to (i.e., aligned to by Sim4) this
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172 exon (i.e., genomic region). At present, merely a synonym for
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173 $obj->feature2().
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174 Returns : An Bio::SeqFeatureI implementing object.
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175 Args :
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176
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177
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178 =cut
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179
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180 sub est_hit {
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181 my $self = shift;
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182 return $self->feature2(@_);
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183 }
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184
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185 1;
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