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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 REVEL
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27
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28 =head1 SYNOPSIS
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29
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30 mv REVEL.pm ~/.vep/Plugins
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31 ./vep -i variations.vcf --plugin REVEL,/path/to/revel/data.tsv.gz
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32
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33 =head1 DESCRIPTION
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34
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35 This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
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36 adds the REVEL score for missense variants to VEP output.
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37
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38 Please cite the REVEL publication alongside the VEP if you use this resource:
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39 https://www.ncbi.nlm.nih.gov/pubmed/27666373
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40
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41 REVEL scores can be downloaded from: https://sites.google.com/site/revelgenomics/downloads
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42 and can be tabix-processed by:
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43
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44 cat revel_all_chromosomes.csv | tr "," "\t" > tabbed_revel.tsv
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45 sed '1s/.*/#&/' tabbed_revel.tsv > new_tabbed_revel.tsv
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46 bgzip new_tabbed_revel.tsv
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47 tabix -f -s 1 -b 2 -e 2 new_tabbed_revel.tsv.gz
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48
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49 The tabix utility must be installed in your path to use this plugin.
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50
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51 =cut
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52 package REVEL;
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53
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54 use strict;
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55 use warnings;
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56
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57 use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
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58
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59 use Bio::EnsEMBL::Variation::Utils::BaseVepTabixPlugin;
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60
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61 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepTabixPlugin);
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62
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63 sub new {
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64 my $class = shift;
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65
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66 my $self = $class->SUPER::new(@_);
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67
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68 $self->expand_left(0);
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69 $self->expand_right(0);
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70
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71 $self->get_user_params();
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72
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73 return $self;
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74 }
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75
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76 sub feature_types {
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77 return ['Transcript'];
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78 }
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79
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80 sub get_header_info {
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81 return { REVEL => 'Rare Exome Variant Ensemble Learner '};
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82 }
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83
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84 sub run {
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85 my ($self, $tva) = @_;
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86 # only for missense variants
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87 return {} unless grep {$_->SO_term eq 'missense_variant'} @{$tva->get_all_OverlapConsequences};
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88
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89 my $vf = $tva->variation_feature;
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90 my $allele = $tva->variation_feature_seq;
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91 my ($res) = grep {
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92 $_->{alt} eq $allele &&
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93 $_->{start} eq $vf->{start} &&
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94 $_->{end} eq $vf->{end} &&
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95 $_->{altaa} eq $tva->peptide
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96 } @{$self->get_data($vf->{chr}, $vf->{start}, $vf->{end})};
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97
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98 return $res ? $res->{result} : {};
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99 }
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100
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101 sub parse_data {
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102 my ($self, $line) = @_;
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103
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104 my ($c, $s, $ref, $alt, $refaa, $altaa, $revel_value) = split /\t/, $line;
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105
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106 return {
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107 alt => $alt,
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108 start => $s,
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109 end => $s,
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110 altaa => $altaa,
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111 result => {
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112 REVEL => $revel_value,
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113 }
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114 };
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115 }
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116
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117 sub get_start {
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118 return $_[1]->{start};
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119 }
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120
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121 sub get_end {
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122 return $_[1]->{end};
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123 }
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124
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125 1;
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