|
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 Blosum62
|
|
|
27
|
|
|
28 =head1 SYNOPSIS
|
|
|
29
|
|
|
30 mv Blosum62.pm ~/.vep/Plugins
|
|
|
31 ./vep -i variations.vcf --plugin Blosum62
|
|
|
32
|
|
|
33 =head1 DESCRIPTION
|
|
|
34
|
|
|
35 This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
|
|
|
36 looks up the BLOSUM 62 substitution matrix score for the reference
|
|
|
37 and alternative amino acids predicted for a missense mutation. It adds
|
|
|
38 one new entry to the VEP's Extra column, BLOSUM62 which is the
|
|
|
39 associated score.
|
|
|
40
|
|
|
41 =cut
|
|
|
42
|
|
|
43 package Blosum62;
|
|
|
44
|
|
|
45 use strict;
|
|
|
46 use warnings;
|
|
|
47
|
|
|
48 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
|
|
|
49
|
|
|
50 my @BLOSUM_62 = qw(
|
|
|
51 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0
|
|
|
52 -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3
|
|
|
53 -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3
|
|
|
54 -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3
|
|
|
55 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1
|
|
|
56 -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2
|
|
|
57 -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2
|
|
|
58 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3
|
|
|
59 -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3
|
|
|
60 -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3
|
|
|
61 -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1
|
|
|
62 -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2
|
|
|
63 -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1
|
|
|
64 -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1
|
|
|
65 -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2
|
|
|
66 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2
|
|
|
67 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0
|
|
|
68 -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3
|
|
|
69 -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1
|
|
|
70 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4
|
|
|
71 );
|
|
|
72
|
|
|
73 my @AAs = qw(A R N D C Q E G H I L K M F P S T W Y V);
|
|
|
74
|
|
|
75 sub new {
|
|
|
76 my $class = shift;
|
|
|
77
|
|
|
78 my $self = $class->SUPER::new(@_);
|
|
|
79
|
|
|
80 # construct a hash representing the matrix for quick lookups
|
|
|
81
|
|
|
82 my $num = @AAs;
|
|
|
83
|
|
|
84 for (my $i = 0; $i < $num; $i++) {
|
|
|
85 for (my $j = 0; $j < $num; $j++) {
|
|
|
86 $self->{matrix}->{$AAs[$i]}->{$AAs[$j]} = $BLOSUM_62[($i * $num) + $j];
|
|
|
87 }
|
|
|
88 }
|
|
|
89
|
|
|
90 return $self;
|
|
|
91 }
|
|
|
92
|
|
|
93 sub version {
|
|
|
94 return '2.3';
|
|
|
95 }
|
|
|
96
|
|
|
97 sub feature_types {
|
|
|
98 return ['Transcript'];
|
|
|
99 }
|
|
|
100
|
|
|
101 sub get_header_info {
|
|
|
102 return {
|
|
|
103 BLOSUM62 => "BLOSUM62 substitution score for the reference and alternative amino acids",
|
|
|
104 };
|
|
|
105 }
|
|
|
106
|
|
|
107 sub run {
|
|
|
108 my ($self, $tva) = @_;
|
|
|
109
|
|
|
110 if ($tva->pep_allele_string && $tva->pep_allele_string =~ /^([A-Z])\/([A-Z])$/) {
|
|
|
111
|
|
|
112 my $score = $self->{matrix}->{$1}->{$2};
|
|
|
113
|
|
|
114 if (defined $score) {
|
|
|
115 return {
|
|
|
116 BLOSUM62 => $score
|
|
|
117 };
|
|
|
118 }
|
|
|
119 }
|
|
|
120
|
|
|
121 return {};
|
|
|
122 }
|
|
|
123
|
|
|
124 1;
|
|
|
125
|
