|
0
|
1 =head1 LICENSE
|
|
|
2
|
|
|
3 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
|
|
|
4 Copyright [2016-2018] EMBL-European Bioinformatics Institute
|
|
|
5
|
|
|
6 Licensed under the Apache License, Version 2.0 (the "License");
|
|
|
7 you may not use this file except in compliance with the License.
|
|
|
8 You may obtain a copy of the License at
|
|
|
9
|
|
|
10 http://www.apache.org/licenses/LICENSE-2.0
|
|
|
11
|
|
|
12 Unless required by applicable law or agreed to in writing, software
|
|
|
13 distributed under the License is distributed on an "AS IS" BASIS,
|
|
|
14 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
|
15 See the License for the specific language governing permissions and
|
|
|
16 limitations under the License.
|
|
|
17
|
|
|
18 =head1 CONTACT
|
|
|
19
|
|
|
20 Ensembl <http://www.ensembl.org/info/about/contact/index.html>
|
|
|
21
|
|
|
22 =cut
|
|
|
23
|
|
|
24 =head1 NAME
|
|
|
25
|
|
|
26 SameCodon
|
|
|
27
|
|
|
28 =head1 SYNOPSIS
|
|
|
29
|
|
|
30 mv SameCodon.pm ~/.vep/Plugins
|
|
|
31 ./vep -i variations.vcf --plugin SameCodon
|
|
|
32
|
|
|
33 =head1 DESCRIPTION
|
|
|
34
|
|
|
35 A VEP plugin that reports existing variants that fall in the same codon.
|
|
|
36
|
|
|
37 =cut
|
|
|
38
|
|
|
39 package SameCodon;
|
|
|
40
|
|
|
41 use strict;
|
|
|
42 use warnings;
|
|
|
43
|
|
|
44 use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
|
|
|
45
|
|
|
46 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
|
|
|
47
|
|
|
48 sub version {
|
|
|
49 return '3.0';
|
|
|
50 }
|
|
|
51
|
|
|
52 sub feature_types {
|
|
|
53 return ['Transcript'];
|
|
|
54 }
|
|
|
55
|
|
|
56 sub get_header_info {
|
|
|
57 return {
|
|
|
58 SameCodon => "Existing variant IDs that fall in the same codon",
|
|
|
59 };
|
|
|
60 }
|
|
|
61
|
|
|
62 sub run {
|
|
|
63
|
|
|
64 my ($self, $tva) = @_;
|
|
|
65
|
|
|
66 if ($self->config->{offline}) {
|
|
|
67 die "A connection to the database is required to use the plugin SameCodon\n";
|
|
|
68 }
|
|
|
69
|
|
|
70 my $tv = $tva->transcript_variation;
|
|
|
71 my $vf = $tv->variation_feature;
|
|
|
72 my ($pep_start, $pep_end) = ($tv->translation_start, $tv->translation_end);
|
|
|
73 my ($vf_start, $vf_end) = ($vf->start, $vf->end);
|
|
|
74
|
|
|
75 return {} unless defined($pep_start) && defined($pep_end);
|
|
|
76
|
|
|
77 my $config = $self->{config};
|
|
|
78
|
|
|
79 # we need to map the TV start and end coords to the genome
|
|
|
80 # needs to be done through the mapper in case the codon spans exons
|
|
|
81 my $mapper = $tv->_mapper();
|
|
|
82
|
|
|
83 return {} unless defined($mapper);
|
|
|
84
|
|
|
85 my @coords = $mapper->pep2genomic($pep_start, $pep_end);
|
|
|
86
|
|
|
87 return {} unless scalar @coords;
|
|
|
88 return {} if grep {!$_->isa('Bio::EnsEMBL::Mapper::Coordinate')} @coords;
|
|
|
89
|
|
|
90 my @results;
|
|
|
91 # we might get multiple "slices" if the codon that the variant falls in spans exons
|
|
|
92 foreach my $coord(@coords) {
|
|
|
93
|
|
|
94 my ($slice_start, $slice_end) = ($coord->start, $coord->end);
|
|
|
95
|
|
|
96 my $sub_slice = $vf->slice->sub_Slice($slice_start, $slice_end);
|
|
|
97 my $vf_adaptor = $vf->slice->_get_VariationFeatureAdaptor();
|
|
|
98 push @results,
|
|
|
99 map {$_->variation_name}
|
|
|
100 grep {
|
|
|
101 $_->variation_name ne $vf->variation_name &&
|
|
|
102 $_->seq_region_start != $vf_start &&
|
|
|
103 $_->seq_region_end != $vf_end &&
|
|
|
104 scalar $mapper->genomic2cds($_->seq_region_start, $_->seq_region_end, 1) >= 1
|
|
|
105 }
|
|
|
106 @{$vf_adaptor->fetch_all_by_Slice_SO_terms($sub_slice)};
|
|
|
107 }
|
|
|
108
|
|
|
109 return {} unless scalar @results;
|
|
|
110
|
|
|
111 return {
|
|
|
112 SameCodon => join ",", @results
|
|
|
113 }
|
|
|
114 }
|
|
|
115
|
|
|
116 1;
|
|
|
117
|
