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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 package Bio::EnsEMBL::Variation::ExternalFeatureVariation;
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22
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23 use strict;
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24 use warnings;
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25
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26 use Bio::EnsEMBL::Variation::ExternalFeatureVariationAllele;
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27 use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(overlap);
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28
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29 use base qw(Bio::EnsEMBL::Variation::RegulationVariation);
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30
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31 sub new {
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32 my $class = shift;
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33
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34 my %args = @_;
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35
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36 # swap a '-external_feature' argument for a '-feature' one for the superclass
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37
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38 for my $arg (keys %args) {
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39 if (lc($arg) eq '-external_feature') {
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40 $args{'-feature'} = delete $args{$arg};
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41 }
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42 }
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43
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44 # call the superclass constructor
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45 my $self = $class->SUPER::new(%args) || return undef;
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46
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47 # rebless the alleles from vfoas to efvas
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48 map { bless $_, 'Bio::EnsEMBL::Variation::ExternalFeatureVariationAllele' }
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49 @{ $self->get_all_ExternalFeatureVariationAlleles };
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50
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51 return $self;
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52 }
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53
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54 sub external_feature_stable_id {
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55 my $self = shift;
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56 return $self->SUPER::feature_stable_id(@_);
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57 }
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58
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59 sub external_feature {
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60 my ($self, $ef) = @_;
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61 return $self->SUPER::feature($ef, 'ExternalFeature');
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62 }
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63
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64 sub add_ExternalFeatureVariationAllele {
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65 my $self = shift;
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66 return $self->SUPER::add_VariationFeatureOverlapAllele(@_);
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67 }
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68
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69 sub get_reference_ExternalFeatureVariationAllele {
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70 my $self = shift;
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71 return $self->SUPER::get_reference_VariationFeatureOverlapAllele(@_);
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72 }
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73
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74 sub get_all_alternate_ExternalFeatureVariationAlleles {
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75 my $self = shift;
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76 return $self->SUPER::get_all_alternate_VariationFeatureOverlapAlleles(@_);
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77 }
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78
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79 sub get_all_ExternalFeatureVariationAlleles {
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80 my $self = shift;
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81 return $self->SUPER::get_all_VariationFeatureOverlapAlleles(@_);
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82 }
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83
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84 sub target_feature_stable_id {
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85 my ($self, $target_feature_stable_id) = @_;
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86
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87 $self->{target_feature_stable_id} = $target_feature_stable_id if $target_feature_stable_id;
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88
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89 unless ($self->{target_feature_stable_id}) {
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90
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91 # try to fetch it from the funcgen database
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92
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93 if (my $species = $self->{adaptor}->db->species) {
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94 for my $entry (
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95 @{ $self->external_feature->get_all_DBEntries($species.'_core_Transcript') },
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96 @{ $self->external_feature->get_all_DBEntries($species.'_core_Gene') } ) {
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97 if (my $id = $entry->primary_id) {
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98
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99 $self->{target_feature_stable_id} = $id;
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100
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101 # there should never be more than one, so we last out of the loop
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102
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103 last;
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104 }
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105 }
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106 }
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107 else {
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108 warn "Failed to get species from adaptor";
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109 }
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110 }
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111
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112 return $self->{target_feature_stable_id};
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113 }
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114
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115 1;
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