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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 TSSDistance
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27
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28 =head1 SYNOPSIS
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29
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30 mv TSSDistance.pm ~/.vep/Plugins
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31 ./vep -i variations.vcf --plugin CCDSFilter
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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 calculates the distance from the transcription
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36 start site for upstream variants.
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37
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38 =cut
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39
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40 package TSSDistance;
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41
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42 use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
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43
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44 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
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45
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46 sub get_header_info {
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47 return {
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48 TSSDistance => "Distance from the transcription start site"
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49 };
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50 }
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51
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52 sub feature_types {
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53 return ['Transcript'];
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54 }
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55
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56 sub variant_feature_types {
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57 return ['BaseVariationFeature'];
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58 }
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59
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60 sub run {
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61 my ($self, $tva) = @_;
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62
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63 my $t = $tva->transcript;
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64 my $vf = $tva->base_variation_feature;
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65
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66 my $dist;
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67
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68 if ($t->strand == 1) {
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69 $dist = $t->start - $vf->end;
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70 }
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71 else {
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72 $dist = $vf->start - $t->end;
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73 }
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74
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75 if ($dist > 0) {
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76 return {
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77 TSSDistance => $dist,
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78 }
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79 }
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80 else {
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81 return {};
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82 }
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83 }
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84
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85 1;
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