|
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 CSN
|
|
|
27
|
|
|
28 =head1 SYNOPSIS
|
|
|
29
|
|
|
30 mv CSN.pm ~/.vep/Plugins
|
|
|
31 ./vep -i variations.vcf --cache --plugin CSN
|
|
|
32
|
|
|
33 =head1 DESCRIPTION
|
|
|
34
|
|
|
35 This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
|
|
|
36 reports Clinical Sequencing Nomenclature (CSN) for variants.
|
|
|
37
|
|
|
38 Each notation is given with reference to the transcript identifier;
|
|
|
39 specify "--plugin CSN,1" to remove this identifier from the CSN string.
|
|
|
40
|
|
|
41 You may also wish to specify "--no_escape" to prevent the "=" in "p.="
|
|
|
42 notations being converted to the URI-escaped equivalent "p.%3D"; doing
|
|
|
43 so may break parsers looking for "=" as a KEY=VALUE separator.
|
|
|
44
|
|
|
45 See http://biorxiv.org/content/early/2015/03/21/016808.1
|
|
|
46
|
|
|
47 =cut
|
|
|
48
|
|
|
49 package CSN;
|
|
|
50
|
|
|
51 use strict;
|
|
|
52 use warnings;
|
|
|
53
|
|
|
54 use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
|
|
|
55 use Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor;
|
|
|
56 use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
|
|
|
57
|
|
|
58 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
|
|
|
59
|
|
|
60 sub new {
|
|
|
61 my $class = shift;
|
|
|
62
|
|
|
63 my $self = $class->SUPER::new(@_);
|
|
|
64
|
|
|
65 # check config is OK
|
|
|
66
|
|
|
67 # FASTA file defined, optimal
|
|
|
68 if(!defined($self->{config}->{fasta})) {
|
|
|
69
|
|
|
70 # offline mode won't work without FASTA
|
|
|
71 die("ERROR: Cannot generate CSN without either a FASTA file (--fasta) or a database connection (--cache or --database)\n") if defined($self->{config}->{offline}) and !defined($self->{config}->{quiet});
|
|
|
72
|
|
|
73 # cache mode will work, but DB will be accessed
|
|
|
74 warn("WARNING: Database will be accessed using this plugin; use a FASTA file (--fasta) for optimal performance") if defined($self->{config}->{cache}) and !defined($self->{config}->{quiet});
|
|
|
75 }
|
|
|
76
|
|
|
77 no warnings 'once';
|
|
|
78 $Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME = 1;
|
|
|
79 no warnings 'once';
|
|
|
80 $Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME = 1;
|
|
|
81
|
|
|
82 $self->{remove_transcript_ID} = $self->params->[0];
|
|
|
83
|
|
|
84 return $self;
|
|
|
85 }
|
|
|
86
|
|
|
87 sub feature_types {
|
|
|
88 return ['Transcript'];
|
|
|
89 }
|
|
|
90
|
|
|
91 sub variant_feature_types {
|
|
|
92 return ['VariationFeature'];
|
|
|
93 }
|
|
|
94
|
|
|
95 sub get_header_info {
|
|
|
96 return { CSN => 'Clinical Sequencing Nomenclature'};
|
|
|
97 }
|
|
|
98
|
|
|
99 sub run {
|
|
|
100 my ($self, $tva) = @_;
|
|
|
101
|
|
|
102 my ($hgvs_c, $hgvs_p) = ($tva->hgvs_transcript || '', $tva->hgvs_protein || '');
|
|
|
103
|
|
|
104 return {} unless $hgvs_c;
|
|
|
105
|
|
|
106 # trim off transcript/protein ID
|
|
|
107 $hgvs_c =~ s/.+\:// if $self->{remove_transcript_ID};
|
|
|
108 $hgvs_p =~ s/.+\://;
|
|
|
109
|
|
|
110 # change Ter to X
|
|
|
111 $hgvs_p =~ s/Ter/X/g;
|
|
|
112
|
|
|
113 # leave just p.=
|
|
|
114 $hgvs_p = 'p.=' if $hgvs_p =~ /p\.\=/;
|
|
|
115
|
|
|
116 # escape
|
|
|
117 $hgvs_p =~ s/\=/\%3D/g unless $self->{config}->{no_escape};
|
|
|
118
|
|
|
119 return { CSN => $hgvs_c.($hgvs_p ? '_'.$hgvs_p : '') };
|
|
|
120 }
|
|
|
121
|
|
|
122 1;
|
