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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::Pipeline::TranscriptEffect;
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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::TranscriptVariation;
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27 use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(MAX_DISTANCE_FROM_TRANSCRIPT);
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28
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29 use base qw(Bio::EnsEMBL::Variation::Pipeline::BaseVariationProcess);
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30
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31 my $DEBUG = 0;
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32
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33 sub run {
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34 my $self = shift;
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35
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36 my $transcript_id = $self->required_param('transcript_stable_id');
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37
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38 my $disambiguate_sn_alleles =
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39 $self->param('disambiguate_single_nucleotide_alleles');
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40
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41 my $variations_to_include;
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42
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43 if (my $vars = $self->param('variations_to_include')) {
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44 # turn the list of variation names into a hash to speed up checking
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45 $variations_to_include = { map { $_ => 1 } @$vars };
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46 }
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47
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48 my $core_dba = $self->get_species_adaptor('core');
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49 my $var_dba = $self->get_species_adaptor('variation');
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50
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51 my $ta = $core_dba->get_TranscriptAdaptor;
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52 my $sa = $core_dba->get_SliceAdaptor;
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53
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54 my $tva = $var_dba->get_TranscriptVariationAdaptor;
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55
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56 my $transcript = $ta->fetch_by_stable_id($transcript_id)
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57 or die "failed to fetch transcript for stable id: $transcript_id";
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58
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59 # we need to include failed variations
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60
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61 $tva->db->include_failed_variations(1);
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62
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63 my $slice = $sa->fetch_by_transcript_stable_id(
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64 $transcript->stable_id,
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65 MAX_DISTANCE_FROM_TRANSCRIPT
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66 ) or die "failed to get slice around transcript: ".$transcript->stable_id;
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67
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68 for my $vf ( @{ $slice->get_all_VariationFeatures },
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69 @{ $slice->get_all_somatic_VariationFeatures } ) {
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70
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71 if (defined $variations_to_include) {
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72 next unless $variations_to_include->{$vf->variation_name};
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73 }
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74
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75 my $tv = Bio::EnsEMBL::Variation::TranscriptVariation->new(
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76 -transcript => $transcript,
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77 -variation_feature => $vf,
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78 -adaptor => $tva,
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79 -disambiguate_single_nucleotide_alleles => $disambiguate_sn_alleles,
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80 );
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81
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82 # if the variation has no effect on the transcript $tv will be undef
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83
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84 if ($tv && ( scalar(@{ $tv->consequence_type }) > 0) ) {
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85 $tva->store($tv);
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86 }
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87 }
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88
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89 return;
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90 }
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91
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92 sub write_output {
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93 my $self = shift;
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94 }
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95
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96 1;
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