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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::PredictionExon - A class representing an Exon from an ab
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24 initio prediction method
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25
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26 =head1 SYNOPSIS
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27
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28 $exon = new Bio::EnsEMBL::PredictionExon(
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29 -START => 100,
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30 -END => 200,
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31 -STRAND => 1,
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32 -SLICE => $slice,
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33 -DBID => $dbID,
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34 -P_VALUE => 23.5,
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35 -SCORE => 99
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36 );
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37
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38 # seq() returns a Bio::Seq
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39 my $seq = $exon->seq->seq();
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40
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41 # peptide() only makes sense within transcript context
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42 my $pep = $exon->peptide($transcript)->seq();
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43
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44 # Normal feature operations can be performed:
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45 $exon = $exon->transform('clone');
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46 $exon->move( $new_start, $new_end, $new_strand );
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47 print $exon->slice->seq_region_name();
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48
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49 =head1 DESCRIPTION
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50
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51 This is a class which represents an prediction exon which is part of a
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52 predcition transcript. See Bio::EnsEMBL:PredictionTranscript
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53
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54 =head1 METHODS
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55
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56 =cut
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57
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58 package Bio::EnsEMBL::PredictionExon;
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59 use vars qw(@ISA);
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60 use strict;
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61
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62 use Bio::EnsEMBL::Feature;
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63 use Bio::EnsEMBL::Exon;
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64 use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
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65 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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66
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67
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68 @ISA = qw(Bio::EnsEMBL::Exon);
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69
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70
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71 =head2 new
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72
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73 Args : see SUPERCLASS Bio::EnsEMBL::Exon
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74 Example : none
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75 Description: create an Exon object
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76 Returntype : Bio::EnsEMBL::PredictionExon
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77 Exceptions : none
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78 Caller : general
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79 Status : Stable
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80
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81 =cut
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82
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83 sub new {
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84 my $class = shift;
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85
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86 $class = ref $class || $class;
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87
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88 my $self = $class->SUPER::new( @_ );
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89
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90 my ( $p_value, $score ) =
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91 rearrange( [ "P_VALUE", "SCORE" ], @_ );
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92
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93 $self->{'p_value'} = $p_value;
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94 $self->{'score'} = $score;
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95
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96 return $self;
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97 }
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98
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99
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100 =head2 score
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101
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102 Arg [1] : string $newval (optional)
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103 The new value to set the score attribute to
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104 Example : $score = $obj->score()
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105 Description: Getter/Setter for the score attribute
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106 Returntype : string
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107 Exceptions : none
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108 Caller : general
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109 Status : Stable
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110
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111 =cut
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112
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113 sub score{
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114 my $self = shift;
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115 $self->{'score'} = shift if(@_);
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116 return $self->{'score'};
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117 }
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118
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119
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120
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121 =head2 p_value
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122
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123 Arg [1] : string $newval (optional)
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124 The new value to set the p_value attribute to
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125 Example : $p_value = $obj->p_value()
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126 Description: Getter/Setter for the p_value attribute
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127 Returntype : string
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128 Exceptions : none
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129 Caller : general
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130 Status : Stable
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131
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132 =cut
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133
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134 sub p_value{
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135 my $self = shift;
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136 $self->{'p_value'} = shift if(@_);
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137 return $self->{'p_value'};
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138 }
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139
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140
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141 =head2 end_phase
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142
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143 Arg [1] : (optional) int $end_phase
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144 Example : $end_phase = $feat->end_phase;
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145 Description: Gets/Sets the end phase of the exon.
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146 end_phase = number of bases from the last incomplete codon of
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147 this exon.
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148 Usually, end_phase = (phase + exon_length)%3
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149 but end_phase could be -1 if the exon is half-coding and its 3
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150 prime end is UTR.
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151 Returntype : int
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152 Exceptions : warning if end_phase is called without an argument and the
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153 value is not set.
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154 Caller : general
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155 Status : Stable
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156
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157 =cut
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158
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159
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160
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161 sub end_phase {
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162 my $self = shift;
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163 if( @_ ) {
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164 throw( "End_phase setting not supported" );
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165 }
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166 return ($self->phase() + $self->length()) % 3;
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167 }
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168
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169
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170 =head2 transform
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171
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172 Arg 1 : String $coordinate_system_name
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173 Arg [2] : String $coordinate_system_version
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174 Description: moves this exon to the given coordinate system. If this exon has
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175 attached supporting evidence, they move as well.
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176 Returntype : Bio::EnsEMBL::Exon
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177 Exceptions : wrong parameters
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178 Caller : general
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179 Status : Stable
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180
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181 =cut
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182
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183
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184 sub transform {
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185 my $self = shift;
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186
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187 # catch for old style transform calls
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188 if( !@_ || ( ref $_[0] && ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" )))) {
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189 throw( "transform needs coordinate systems details now," .
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190 "please use transfer" );
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191 }
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192
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193 my $new_exon = Bio::EnsEMBL::Feature::transform( $self, @_ );
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194 return undef unless $new_exon;
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195
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196 #dont want to share the same sequence cache
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197 delete $new_exon->{'_seq_cache'};
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198
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199 return $new_exon;
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200 }
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201
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202
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203
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204 =head2 transfer
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205
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206 Arg [1] : Bio::EnsEMBL::Slice $destination_slice
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207 Example : none
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208 Description: Moves this Exon to given target slice coordinates. If Features
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209 are attached they are moved as well. Returns a new exon.
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210 Returntype : Bio::EnsEMBL::Gene
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211 Exceptions : none
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212 Caller : general
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213 Status : Stable
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214
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215 =cut
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216
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217 sub transfer {
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218 my $self = shift;
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219
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220 my $new_exon = Bio::EnsEMBL::Feature::transfer( $self, @_ );
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221 return undef unless $new_exon;
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222
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223 #dont want to share the same sequence cache
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224 delete $new_exon->{'_seq_cache'};
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225
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226 return $new_exon;
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227 }
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228
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229
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230 =head2 add_supporting_features
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231
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232 Description: For compatibility with Bio::EnsEMBL::Exon
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233 Does nothing.
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234 Returntype : none
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235 Status : Stable
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236
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237 =cut
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238
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239 sub add_supporting_features { }
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240
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241
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242 =head2 get_all_supporting_features
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243
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244 Description: For compatibility with Bio::EnsEMBL::Exon
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245 Does nothing and returns empty list
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246 Returntype : empty list.
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247 Status : Stable
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248
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249 =cut
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250
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251 sub get_all_supporting_features { return []; }
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252
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253
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254 =head2 find_supporting_evidence
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255
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256 Description: For compatibility with Bio::EnsEMBL::Exon
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257 Does nothing.
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258 Returntype : empty list.
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259 Status : Stable
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260
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261 =cut
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262
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263 sub find_supporting_evidence { return []; }
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264
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265
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266 1;
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