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1 =head1 LICENSE
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2
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3 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
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4 Copyright [2016-2018] EMBL-European Bioinformatics Institute
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5
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6 Licensed under the Apache License, Version 2.0 (the "License");
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7 you may not use this file except in compliance with the License.
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8 You may obtain a copy of the License at
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9
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10 http://www.apache.org/licenses/LICENSE-2.0
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11
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12 Unless required by applicable law or agreed to in writing, software
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13 distributed under the License is distributed on an "AS IS" BASIS,
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14 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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15 See the License for the specific language governing permissions and
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16 limitations under the License.
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17
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18 =head1 CONTACT
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19
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20 Ensembl <http://www.ensembl.org/info/about/contact/index.html>
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21
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22 =cut
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23
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24 =head1 NAME
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25
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26 LOVD
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27
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28 =head1 SYNOPSIS
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29
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30 mv LOVD.pm ~/.vep/Plugins
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31 ./vep -i variations.vcf --plugin LOVD
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32
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33 =head1 DESCRIPTION
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34
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35 A VEP plugin that retrieves LOVD variation data from http://www.lovd.nl/.
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36
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37 Please be aware that LOVD is a public resource of curated variants, therefore
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38 please respect this resource and avoid intensive querying of their databases
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39 using this plugin, as it will impact the availability of this resource for
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40 others.
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41
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42 =cut
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43
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44 package LOVD;
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45
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46 use strict;
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47 use warnings;
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48 use LWP::UserAgent;
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49
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50 use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
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51
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52 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
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53
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54 sub version {
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55 return '2.5';
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56 }
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57
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58 sub feature_types {
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59 return ['Transcript'];
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60 }
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61
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62 sub get_header_info {
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63 return {
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64 LOVD => "LOVD variant ID",
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65 };
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66 }
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67
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68 sub run {
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69 my ($self, $tva) = @_;
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70
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71 $self->{has_cache} = 1;
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72
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73 my %hg_assembly = ( 'grch37' => 'hg19', 'grch38' => 'hg38' );
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74 my $assembly = lc($self->{config}->{assembly});
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75
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76 # only works on human
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77 die("ERROR: LOVD plugin works only on human data") unless $self->{config}->{species} =~ /human|homo/i;
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78
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79 # only work on 2 human assemblies
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80 die("ERROR: LOVD plugin works only on human assemblies ".join(' and ', keys(%hg_assembly))) unless $hg_assembly{$assembly};
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81
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82 # get the VF object
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83 my $vf = $tva->variation_feature;
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84 return {} unless defined $vf;
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85
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86 # set up a LWP UserAgent
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87 my $ua = LWP::UserAgent->new;
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88 $ua->env_proxy;
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89
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90 my $chr = $vf->{chr};
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91 $chr =~ s/^chr//;
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92
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93 my $locus = sprintf('chr%s:%s_%s', $chr, $vf->{start}, $vf->{end});
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94
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95 my $data;
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96
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97 # check the cache
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98 if(!exists($self->{lovd_cache}->{$locus})) {
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99
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100 # construct a LOVD URL
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101 my $url = sprintf('http://www.lovd.nl/search.php?build=%s&position=%s', $hg_assembly{$assembly}, $locus);
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102
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103 # get the accession (only need the head to get the redirect URL that contains the accession)
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104 my $response = $ua->get($url);
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105
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106 if($response->is_success) {
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107
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108 # parse the data into a hash
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109 for(grep {$_ !~ /hg_build/} split /\cJ/, $response->decoded_content) {
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110 s/\"//g;
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111
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112 my ($build, $pos, $gene, $acc, $dna, $url) = split /\t/;
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113
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114 $data = join(',', $gene, $acc, $dna)
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115 }
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116
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117 $self->{lovd_cache}->{$locus} = $data;
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118 }
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119 }
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120 else {
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121 $data = $self->{lovd_cache}->{$locus};
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122 }
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123
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124 return $data ? { LOVD => $data } : {};
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125 }
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126
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127 1;
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128
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