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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::Variation::BaseVariationFeatureOverlapAllele
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24
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25 =head1 SYNOPSIS
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26
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27 use Bio::EnsEMBL::Variation::BaseVariationFeatureOverlapAllele;
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28
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29 my $bvfoa = Bio::EnsEMBL::Variation::BaseVariationFeatureOverlapAllele->new(
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30 -base_variation_feature_overlap => $bvfo,
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31 -is_reference => 0,
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32 );
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33
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34 print "consequence SO terms: ", (join ",", map { $_->SO_term } @{ $bvfoa->get_all_OverlapConsequences }), "\n";
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35
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36 =head1 DESCRIPTION
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37
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38 A BaseVariationFeatureOverlapAllele object represents a single allele of a
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39 BaseVariationFeatureOverlap. It is the super-class of variation feature specific
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40 classes such as VariationFeatureOverlapAllele and StructuralVariationOverlapAllele
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41 and contains methods not specific to any particular variation feature type.
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42 Ordinarily you will not create these objects yourself, but instead you would
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43 create one of the more specific subclasses.
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44
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45 =cut
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46
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47 package Bio::EnsEMBL::Variation::BaseVariationFeatureOverlapAllele;
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48
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49 use strict;
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50 use warnings;
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51
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52 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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53 use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
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54 use Bio::EnsEMBL::Utils::Exception qw(throw);
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55 use Bio::EnsEMBL::Variation::Utils::Constants qw(%OVERLAP_CONSEQUENCES);
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56 use Scalar::Util qw(weaken);
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57
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58 =head2 new
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59
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60 Arg [-BASE_VARIATION_FEATURE_OVERLAP] :
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61 The Bio::EnsEMBL::BaseVariationFeatureOverlap with which this allele is
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62 associated
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63
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64 Arg [-IS_REFERENCE] :
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65 A flag indicating if this allele is the reference allele or not
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66
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67 Example :
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68 my $bvfoa = Bio::EnsEMBL::Variation::BaseVariationFeatureOverlapAllele->new(
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69 -base_variation_feature_overlap => $bvfo,
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70 -is_reference => 0
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71 );
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72
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73 Description: Constructs a new BaseVariationFeatureOverlapAllele instance given a
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74 BaseVariationFeatureOverlap and a flag indicating if this is the
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75 reference allele
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76 Returntype : A new Bio::EnsEMBL::Variation::BaseVariationFeatureOverlapAllele instance
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77 Exceptions : throws unlessBASE_VARIATION_FEATURE_OVERLAP is supplied
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78 Status : At Risk
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79
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80 =cut
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81
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82 sub new {
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83 my $class = shift;
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84
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85 my (
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86 $base_variation_feature_overlap,
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87 $is_reference
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88 ) = rearrange([qw(
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89 BASE_VARIATION_FEATURE_OVERLAP
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90 IS_REFERENCE
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91 )], @_);
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92
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93 assert_ref($base_variation_feature_overlap, 'Bio::EnsEMBL::Variation::BaseVariationFeatureOverlap');
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94
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95 my $self = bless {
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96 base_variation_feature_overlap => $base_variation_feature_overlap,
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97 is_reference => $is_reference,
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98 }, $class;
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99
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100 # avoid a memory leak, because the bvfo also has a reference to us
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101 weaken $self->{base_variation_feature_overlap};
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102
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103 return $self;
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104 }
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105
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106 sub new_fast {
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107 my ($class, $hashref) = @_;
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108 my $self = bless $hashref, $class;
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109 # avoid a memory leak, because the bvfo also has a reference to us
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110 weaken $self->{base_variation_feature_overlap} if $self->{base_variation_feature_overlap};
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111 return $self;
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112 }
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113
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114 =head2 base_variation_feature_overlap
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115
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116 Description: Get/set the associated BaseVariationFeatureOverlap
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117 Returntype : Bio::EnsEMBL::Variation::BaseVariationFeatureOverlap
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118 Exceptions : throws if the argument is the wrong type
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119 Status : At Risk
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120
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121 =cut
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122
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123 sub base_variation_feature_overlap {
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124 my ($self, $bvfo) = @_;
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125
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126 if ($bvfo) {
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127 assert_ref($bvfo, 'Bio::EnsEMBL::Variation::BaseVariationFeatureOverlap');
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128 $self->{base_variation_feature_overlap} = $bvfo;
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129 # avoid a memory leak, because the bvfo also has a reference to us
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130 weaken $self->{base_variation_feature_overlap};
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131 }
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132
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133 return $self->{base_variation_feature_overlap};
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134 }
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135
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136 =head2 base_variation_feature
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137
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138 Description: Get the associated BaseVariationFeature
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139 Returntype : Bio::EnsEMBL::Variation::BaseVariationFeature
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140 Exceptions : none
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141 Status : At Risk
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142
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143 =cut
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144
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145 sub base_variation_feature {
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146 my $self = shift;
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147 return $self->base_variation_feature_overlap->base_variation_feature(@_);
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148 }
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149
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150 =head2 feature
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151
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152 Description: Get the associated Feature
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153 Returntype : Bio::EnsEMBL::Feature (or relevant subclass)
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154 Exceptions : none
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155 Status : At Risk
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156
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157 =cut
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158
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159 sub feature {
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160 my $self = shift;
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161 return $self->base_variation_feature_overlap->feature(@_);
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162 }
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163
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164 =head2 is_reference
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165
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166 Args [1] : A boolean value
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167 Description: Get/set a flag indicating if this allele is the reference allele
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168 Returntype : bool
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169 Exceptions : none
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170 Status : At Risk
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171
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172 =cut
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173
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174 sub is_reference {
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175 my ($self, $is_reference) = @_;
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176 $self->{is_reference} = $is_reference if defined $is_reference;
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177 return $self->{is_reference};
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178 }
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179
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180 =head2 get_all_OverlapConsequences
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181
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182 Description: Get a list of all the OverlapConsequences of this allele, calculating them
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183 on the fly if necessary
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184 Returntype : listref of Bio::EnsEMBL::Variation::OverlapConsequence objects
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185 Exceptions : none
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186 Status : At Risk
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187
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188 =cut
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189
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190 sub get_all_OverlapConsequences {
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191 my $self = shift;
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192
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193 unless ($self->{overlap_consequences}) {
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194
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195 # calculate consequences on the fly
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196
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197 my $cons = [];
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198
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199 my $assigned_tier;
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200
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201 # loop over all the possible consequences
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202 for my $oc (@{$self->get_sorted_OverlapConsequences}) {
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203
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204 last if defined($assigned_tier) and $oc->tier > $assigned_tier;
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205
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206 # check that this consequence applies to this type of variation feature
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207
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208 if ($oc->variant_feature_class && $self->base_variation_feature->isa($oc->variant_feature_class)) {
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209
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210 # check that this consequence applies to this type of feature
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211
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212 if ($self->feature->isa($oc->feature_class)) {
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213
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214 # if so, check if the predicate of this consequence holds for this bvfoa
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215 my $check = $oc->predicate->($self);
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216
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217 #print STDERR $self->base_variation_feature->variation_name." ".$oc->{SO_term}." ".$self->feature->stable_id. " $check\n";
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218
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219 if ($check) {
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220 push @$cons, $oc;
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221 $assigned_tier = $oc->tier;
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222 }
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223 }
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224 }
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225 }
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226
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227 $self->{overlap_consequences} = $cons;
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228 }
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229
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230 return $self->{overlap_consequences};
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231 }
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232
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233 =head2 add_OverlapConsequence
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234
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235 Arg [1] : Bio::EnsEMBL::Variation::OverlapConsequence instance
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236 Description: Add an OverlapConsequence to this allele's list
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237 Returntype : none
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238 Exceptions : throws if the argument is the wrong type
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239 Status : At Risk
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240
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241 =cut
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242
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243 sub add_OverlapConsequence {
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244 my ($self, $oc) = @_;
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245 assert_ref($oc, 'Bio::EnsEMBL::Variation::OverlapConsequence');
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246 $self->{overlap_consequences} ||= [];
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247 push @{ $self->{overlap_consequences} }, $oc;
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248 }
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249
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250 sub SO_isa {
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251 my ($self, $query) = @_;
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252
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253 if (my $adap = $self->base_variation_feature_overlap->{adaptor}) {
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254 if (my $ota = $adap->db->dnadb->get_OntologyTermAdaptor) {
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255 my $term = $ota->fetch_by_accession();
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256 my @parents = $ota->fetch_by_child_term($term);
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257 }
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258 }
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259
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260 for my $cons (@{ $self->get_all_OverlapConsequences }) {
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261 if ($cons->SO_term eq $query) {
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262 return 1;
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263 }
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264 }
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265 }
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266
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267 sub get_sorted_OverlapConsequences {
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268 my $self = shift;
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269
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270 if(!defined($self->base_variation_feature_overlap->adaptor->{sorted_cons})) {
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271 my @sorted = sort {$a->tier <=> $b->tier} values %OVERLAP_CONSEQUENCES;
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272 $self->base_variation_feature_overlap->adaptor->{sorted_cons} = \@sorted;
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273 }
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274
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275 return $self->base_variation_feature_overlap->adaptor->{sorted_cons};
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276 }
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277
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278 1;
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279
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