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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2015 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 Ensembl <http://www.ensembl.org/info/about/contact/index.html>
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14
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15 =cut
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16
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17 =head1 NAME
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18
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19 DAS
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20
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21 =head1 SYNOPSIS
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22
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23 mv DAS.pm ~/.vep/Plugins
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24 ./vep -i variations.vcf --plugin DAS,<DAS_server>,<DAS_source>,<proxy>
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25
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26 =head1 DESCRIPTION
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27
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28 A simple VEP plugin that checks for DAS features overlapping variants. Currently assumes that
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29 the assemblies match, and doesn't do any smart fetching of chunks of features (i.e. the plugin
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30 will query the DAS server once for every variant in the input file).
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31
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32 You can run multiple instances of this plugin at the same time so you can query multiple DAS
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33 servers and sources. If you are querying multiple sources from the same server it is
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34 convenient to store the server name in an environment variable to avoid specifying it
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35 multiple times, e.g.:
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36
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37 export DAS="http://somewhere/das"
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38 ./vep -i variations.vcf --plugin DAS,$DAS,source1 --plugin DAS,$DAS,source2
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39
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40 Requires the Bio::Das::Lite module from CPAN.
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41
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42 =cut
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43
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44 package DAS;
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45
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46 use strict;
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47 use warnings;
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48
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49 use Bio::Das::Lite;
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50 use Data::Dumper;
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51
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52 use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
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53
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54 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
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55
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56 sub get_header_info {
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57 my $self = shift;
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58 return {
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59 $self->header => $self->{source}." features from DAS server ".$self->{server},
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60 };
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61 }
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62
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63 sub feature_types {
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64 return ['Transcript','RegulatoryFeature','MotifFeature','Intergenic'];
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65 }
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66
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67 sub new {
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68 my $class = shift;
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69
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70 my $self = $class->SUPER::new(@_);
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71
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72 my ($server, $source, $proxy) = @{ $self->params };
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73
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74 # strip off any trailing slash from the server URL
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75 $server =~ s/\/$//;
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76
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77 $self->{das} = Bio::Das::Lite->new({
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78 timeout => 10000,
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79 dsn => "$server/$source",
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80 http_proxy => $proxy,
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81 }) || die "Failed to connect to DAS source: $server/$source";
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82
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83 $self->{source} = $source;
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84 $self->{server} = $server;
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85
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86 return $self;
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87 }
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88
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89 sub header {
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90 my $self = shift;
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91 return 'DAS_'.$self->{source};
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92 }
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93
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94 sub run {
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95 my ($self, $vfoa) = @_;
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96
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97 my $vf = $vfoa->variation_feature;
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98
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99 my $segment = $vf->seq_region_name .':'.$vf->seq_region_start.','.$vf->seq_region_end;
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100
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101 # cache the results on the variation feature, making sure the cache key is unique given
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102 # that there may be multiple DAS plugins running
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103
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104 my $cache_key = '_vep_das_cache_'.$self->{server}.$self->{source};
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105
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106 unless (exists $vf->{$cache_key}->{$segment}) {
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107
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108 $vf->{$cache_key}->{$segment} = [];
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109
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110 if (my $response = $self->{das}->features($segment)) {
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111 for my $url (keys %$response) {
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112 if (ref $response->{$url} eq 'ARRAY') {
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113 for my $feat (@{ $response->{$url} }) {
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114 push @{ $vf->{$cache_key}->{$segment} }, $feat->{feature_label}.'('.$feat->{type}.')';
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115 }
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116 }
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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 my $res = join ',', @{ $vf->{$cache_key}->{$segment} };
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122
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123 return $res ? {$self->header => $res} : {};
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124 }
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125
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126 1;
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127
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