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1 # BioPerl module for Bio::PrimedSeq
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2 #
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3 # Cared for by Chad Matsalla <bioinformatics1@dieselwurks.com>
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4 #
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5 # Copyright Chad Matsalla
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8
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9 # POD documentation - main docs before the code
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10
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11 =head1 Bio::Seq::PrimedSeq
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12
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13 Bio::Seq::PrimedSeq - A representation of a sequence and two primers flanking a
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14 target region for amplification
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15
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16 =head1 SYNOPSIS
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17
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18 # create a sequence
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19 my $sequence = "ctagctagctagctagctagctagctagctgatcgtagctagctagct";
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20 # create left and right primer seqfeatures
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21 # unfortunately, I haven't created constructors for these yet.
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22 my $left = Bio::SeqFeature::Primer();
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23 my $right = Bio::SeqFeature::Primer();
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24 # now create the PrimedSeq
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25 $primedseq = new Bio::Seq::PrimedSeq(
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26 -seq => $sequence,
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27 -display_id => "chads_fantastic_sequence",
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28 -LEFT_PRIMER => $left,
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29 -RIGHT_PRIMER => $right,
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30 -TARGET => '513,26'
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31 -PRIMER_PRODUCT_SIZE_RANGE => '100-500'
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32 -PRIMER_FILE_FLAG => '0'
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33 -PRIMER_LIBERAL_BASE => '1'
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34 -PRIMER_NUM_RETURN => '1'
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35 -PRIMER_FIRST_BASE_INDEX => '1'
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36 -PRIMER_EXPLAIN_FLAG => '1'
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37 -PRIMER_PRODUCT_SIZE => '185'
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38 );
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39 # get the amplified region
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40 my $amplified_sequence = $primed_seq->get_amplified_sequence();
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41
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42 =head1 DESCRIPTION
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43
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44 This module is a slightly glorified capsule containg a primed seqBuence. It was
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45 created to address the fact that a primer is more the a seqfeature and there
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46 need to be ways to represent the primer-sequence complex and the behaviors and
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47 attributes that are associated with the complex.
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48
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49 =head1 FEEDBACK
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50
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51 User feedback is an integral part of the evolution of this and other
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52 Bioperl modules. Send your comments and suggestions preferably to one
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53 of the Bioperl mailing lists. Your participation is much appreciated.
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54
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55 bioperl-l@bioperl.org - General discussion
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56 http://bio.perl.org/MailList.html - About the mailing lists
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57
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58 =head2 Reporting Bugs
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59
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60 Report bugs to the Bioperl bug tracking system to help us keep track
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61 the bugs and their resolution. Bug reports can be submitted via email
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62 or the web:
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63
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64 bioperl-bugs@bio.perl.org
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65 http://bugzilla.bioperl.org/
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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
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70 methods. Internal methods are usually preceded with a _
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71
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72 =cut
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73
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74
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75 # Let the code begin...
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76
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77
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78 package Bio::Seq::PrimedSeq;
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79 use vars qw(@ISA);
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80 use strict;
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81
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82 use Bio::RangeI;
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83
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84 @ISA = qw(Bio::Seq);
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85
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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 : $primed_sequence = new Bio::SeqFeature::Primer( -seq => $sequence,
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91 -left_primer => $left_primer,
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92 -right_primer => $right_primer);
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93 Function: A constructor for an object representing a primed sequence
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94 Returns : A Bio::Seq::PrimedSeq object
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95 Args :
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96 -seq => a Bio::Seq object
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97 -left_primer => a Bio::SeqFeature::Primer object
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98 -right_primer => a Bio::SeqFeature::Primer object
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99 Many other parameters can be included including all of the output
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100 parameters from the primer3 program.
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101 Developer Notes: This is incomplete and doesn't work. As of ISMB2002 I am working on it.
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102
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103
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104 =cut
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105
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106 sub new {
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107 my($class,@args) = @_;
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108 my %arguments = @args;
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109 my $self = $class->SUPER::new(@args);
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110 # these are the absolute minimum components required to make
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111 # a primedseq
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112 my $newkey;
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113 foreach my $key (sort keys %arguments) {
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114 ($newkey = $key) =~ s/-//;
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115 $self->{$newkey} = $arguments{$key};
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116 push @{$self->{arguments}},$newkey;
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117 }
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118 # and now the insurance- make sure that things are ok
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119 if (!$self->{target_sequence} || !$self->{left_primer} || !$self->{right_primer} ) {
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120 $self->throw("You must provide a target_sequence, left_primer, and right_primer to create this object.");
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121 }
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122 if (ref($self->{target_sequence}) ne "Bio::Seq") {
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123 $self->throw("The target_sequence must be a Bio::Seq to create this object.");
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124 }
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125 if (ref($self->{left_primer}) ne "Bio::SeqFeature::Primer" || ref($self->{right_primer}) ne "Bio::SeqFeature::Primer") {
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126 $self->throw("You must provide a left_primer and right_primer, both as Bio::SeqFeature::Primer to create this object.");
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127 }
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128 return $self;
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129 }
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130
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131
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132 =head2 get_left_primer
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133
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134 Title : get_left_primer();
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135 Usage : $left_primer = $primedseq->get_left_primer();
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136 Function: A getter for the left primer in thie PrimedSeq object.
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137 Returns : A Bio::SeqFeature::Primer object
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138 Args : None.
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139
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140 =cut
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141
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142 sub get_left_primer() {
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143 my $self = shift;
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144
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145
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146
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147
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148 }
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149
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150
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151
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152
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153
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154
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155
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156
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157
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158
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159
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160
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161 =head2 Bio::RangeI methods
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162
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163 List of interfaces inherited from Bio::RangeI (see L<Bio::RangeI>
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164 for details).
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165
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166 =head2 start
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167
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168 Title : start
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169 Usage : $start = $feat->start
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170 Function: Returns the start coordinate of the feature
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171 Returns : integer
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172 Args : none
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173 Developer Notes:
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174 This is entirely dependent on the sequence to which this primer is attached!
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175 I think that there could be trouble if one takes this primer from sequence 1
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176 and naively place it on sequence 2 without updating this
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177 ** This is incomplete at this time.
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178 =cut
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179
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180 sub start() {
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181 my $self = shift;
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182
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183
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184 }
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185
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186
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187
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188
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189 =head2 end
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190
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191 Title : end
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192 Usage : $end = $feat->end
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193 Function: Returns the end coordinate of the feature
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194 Returns : integer
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195 Args : none
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196 Developer Notes:
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197 ** This is incomplete at this time.
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198 =cut
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199
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200 sub end() {
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201 my $self = shift;
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202
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203
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204 }
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205
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206 =head2 strand
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207
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208 Title : strand
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209 Usage : $strand = $feat->strand()
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210 Function: Returns strand information, being 1,-1 or 0
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211 Returns : -1,1 or 0
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212 Args : none
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213 Developer Notes:
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214 ** This is incomplete at this time.
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215
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216
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217 =cut
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218
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219 sub strand() {
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220 my $self = shift;
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221 }
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222
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223
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224 =head2 SeqFeatureI specific methods
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225
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226 New method interfaces.
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227
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228 =head2 sub_SeqFeature
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229
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230 Title : sub_SeqFeature
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231 Usage : @feats = $feat->sub_SeqFeature();
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232 Function: Returns an array of sub Sequence Features
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233 Returns : An array
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234 Args : none
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235
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236 =cut
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237
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238 sub sub_SeqFeature{
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239 my ($self,@args) = @_;
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240
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241 $self->throw_not_implemented();
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242 }
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243
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244 =head2 display_id
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245
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246 Title : display_id
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247 Usage : $name = $feat->display_id()
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248 Function: Returns the human-readable ID of the
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249 feature for displays.
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250 Returns : a string
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251 Args : none
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252
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253 =cut
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254
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255 sub display_id {
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256 my ($self,@args) = @_;
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257 $self->throw_not_implemented();
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258 }
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259
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260 =head2 primary_tag
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261
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262 Title : primary_tag
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263 Usage : $tag = $feat->primary_tag()
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264 Function: Returns the primary tag for a feature,
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265 eg 'exon'
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266 Returns : a string
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267 Args : none
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268
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269
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270 =cut
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271
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272 sub primary_tag{
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273 my ($self,@args) = @_;
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274
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275 $self->throw_not_implemented();
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276
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277 }
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278
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279 =head2 source_tag
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280
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281 Title : source_tag
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282 Usage : $tag = $feat->source_tag()
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283 Function: Returns the source tag for a feature,
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284 eg, 'genscan'
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285 Returns : a string
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286 Args : none
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287
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288
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289 =cut
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290
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291 sub source_tag{
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292 my ($self,@args) = @_;
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293
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294 $self->throw_not_implemented();
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295 }
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296
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297 =head2 has_tag
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298
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299 Title : has_tag
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300 Usage : $tag_exists = $self->has_tag('some_tag')
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301 Function:
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302 Returns : TRUE if the specified tag exists, and FALSE otherwise
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303 Args :
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304
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305
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306 =cut
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307
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308 sub has_tag{
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309 my ($self,@args) = @_;
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310
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311 $self->throw_not_implemented();
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312
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313 }
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314
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315 =head2 each_tag_value
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316
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317 Title : each_tag_value
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318 Usage : @values = $self->each_tag_value('some_tag')
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319 Function:
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320 Returns : An array comprising the values of the specified tag.
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321 Args :
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322
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323
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324 =cut
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325
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326 sub each_tag_value {
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327 my ($self,@args) = @_;
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328
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329 $self->throw_not_implemented();
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330 }
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331
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332 =head2 all_tags
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333
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334 Title : all_tags
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335 Usage : @tags = $feat->all_tags()
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336 Function: gives all tags for this feature
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337 Returns : an array of strings
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338 Args : none
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339
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340
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341 =cut
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342
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343 sub all_tags{
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344 my ($self,@args) = @_;
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345
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346 $self->throw_not_implemented();
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347 }
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348
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349 =head2 gff_string
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350
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351 Title : gff_string
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352 Usage : $str = $feat->gff_string;
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353 $str = $feat->gff_string($gff_formatter);
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354 Function: Provides the feature information in GFF format.
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355
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356 The implementation provided here returns GFF2 by default. If you
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357 want a different version, supply an object implementing a method
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358 gff_string() accepting a SeqFeatureI object as argument. E.g., to
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359 obtain GFF1 format, do the following:
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360
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361 my $gffio = Bio::Tools::GFF->new(-gff_version => 1);
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362 $gff1str = $feat->gff_string($gff1io);
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363
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364 Returns : A string
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365 Args : Optionally, an object implementing gff_string().
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366
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367
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368 =cut
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369
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370 sub gff_string{
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371 my ($self,$formatter) = @_;
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372
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373 $formatter = $self->_static_gff_formatter unless $formatter;
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374 return $formatter->gff_string($self);
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375 }
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376
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377 my $static_gff_formatter = undef;
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378
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379 =head2 _static_gff_formatter
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380
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381 Title : _static_gff_formatter
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382 Usage :
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383 Function:
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384 Example :
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385 Returns :
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386 Args :
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387
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388
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389 =cut
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390
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391 sub _static_gff_formatter{
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392 my ($self,@args) = @_;
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393
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394 if( !defined $static_gff_formatter ) {
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395 $static_gff_formatter = Bio::Tools::GFF->new('-gff_version' => 2);
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396 }
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397 return $static_gff_formatter;
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398 }
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399
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400
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401
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402 =head1 RangeI methods
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403
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404 These methods are inherited from RangeI and can be used
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405 directly from a SeqFeatureI interface. Remember that a
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406 SeqFeature is-a RangeI, and so wherever you see RangeI you
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407 can use a feature ($r in the below documentation).
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408
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409 =head2 overlaps
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410
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411 Title : overlaps
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412 Usage : if($feat->overlaps($r)) { do stuff }
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413 if($feat->overlaps(200)) { do stuff }
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414 Function: tests if $feat overlaps $r
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415 Args : a RangeI to test for overlap with, or a point
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416 Returns : true if the Range overlaps with the feature, false otherwise
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417
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418
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419 =head2 contains
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420
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421 Title : contains
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422 Usage : if($feat->contains($r) { do stuff }
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423 Function: tests whether $feat totally contains $r
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424 Args : a RangeI to test for being contained
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425 Returns : true if the argument is totaly contained within this range
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426
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427
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428 =head2 equals
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429
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430 Title : equals
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431 Usage : if($feat->equals($r))
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432 Function: test whether $feat has the same start, end, strand as $r
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433 Args : a RangeI to test for equality
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434 Returns : true if they are describing the same range
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435
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436
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437 =head1 Geometrical methods
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438
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439 These methods do things to the geometry of ranges, and return
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440 triplets (start, stop, strand) from which new ranges could be built.
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441
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442 =head2 intersection
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443
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444 Title : intersection
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445 Usage : ($start, $stop, $strand) = $feat->intersection($r)
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446 Function: gives the range that is contained by both ranges
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447 Args : a RangeI to compare this one to
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448 Returns : nothing if they do not overlap, or the range that they do overlap
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449
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450 =head2 union
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451
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452 Title : union
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453 Usage : ($start, $stop, $strand) = $feat->union($r);
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454 : ($start, $stop, $strand) = Bio::RangeI->union(@ranges);
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455 Function: finds the minimal range that contains all of the ranges
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456 Args : a range or list of ranges to find the union of
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457 Returns : the range containing all of the ranges
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458
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459 =cut
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460
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461 =head2 location
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462
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463 Title : location
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464 Usage : my $location = $seqfeature->location()
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465 Function: returns a location object suitable for identifying location
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466 of feature on sequence or parent feature
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467 Returns : Bio::LocationI object
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468 Args : none
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469
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470
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471 =cut
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472
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473 sub location {
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474 my ($self) = @_;
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475
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476 $self->throw_not_implemented();
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477 }
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478
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479
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480 1;
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