|
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 GO
|
|
|
27
|
|
|
28 =head1 SYNOPSIS
|
|
|
29
|
|
|
30 mv GO.pm ~/.vep/Plugins
|
|
|
31 ./vep -i variations.vcf --plugin GO
|
|
|
32
|
|
|
33 =head1 DESCRIPTION
|
|
|
34
|
|
|
35 A VEP plugin that retrieves Gene Ontology terms associated with
|
|
|
36 transcripts/translations via the Ensembl API. Requires database connection.
|
|
|
37
|
|
|
38 =cut
|
|
|
39
|
|
|
40 package GO;
|
|
|
41
|
|
|
42 use strict;
|
|
|
43 use warnings;
|
|
|
44
|
|
|
45 use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
|
|
|
46
|
|
|
47 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
|
|
|
48
|
|
|
49 sub new {
|
|
|
50 my $class = shift;
|
|
|
51
|
|
|
52 my $self = $class->SUPER::new(@_);
|
|
|
53
|
|
|
54 # connect to DB for offline users
|
|
|
55 my $config = $self->{config};
|
|
|
56 my $reg = $config->{reg};
|
|
|
57
|
|
|
58 if(!defined($self->{config}->{sa})) {
|
|
|
59 $reg = 'Bio::EnsEMBL::Registry';
|
|
|
60 $reg->load_registry_from_db(
|
|
|
61 -host => $config->{host},
|
|
|
62 -user => $config->{user},
|
|
|
63 -pass => $config->{password},
|
|
|
64 -port => $config->{port},
|
|
|
65 -db_version => $config->{db_version},
|
|
|
66 -species => $config->{species} =~ /^[a-z]+\_[a-z]+/i ? $config->{species} : undef,
|
|
|
67 -verbose => $config->{verbose},
|
|
|
68 -no_cache => $config->{no_slice_cache},
|
|
|
69 );
|
|
|
70 }
|
|
|
71
|
|
|
72 return $self;
|
|
|
73 }
|
|
|
74
|
|
|
75 sub version {
|
|
|
76 return 73;
|
|
|
77 }
|
|
|
78
|
|
|
79 sub feature_types {
|
|
|
80 return ['Transcript'];
|
|
|
81 }
|
|
|
82
|
|
|
83 sub get_header_info {
|
|
|
84 return { 'GO' => 'GO terms associated with protein product'};
|
|
|
85 }
|
|
|
86
|
|
|
87 sub run {
|
|
|
88 my ($self, $tva) = @_;
|
|
|
89
|
|
|
90 my $tr = $tva->transcript->translation;
|
|
|
91 return {} unless defined($tr);
|
|
|
92
|
|
|
93 my $entries = $tr->get_all_DBEntries('GO');
|
|
|
94
|
|
|
95 my $string = join(",", map {$_->display_id.':'.$_->description} @$entries);
|
|
|
96 $string =~ s/\s+/\_/g;
|
|
|
97
|
|
|
98 return { GO => $string };
|
|
|
99 }
|
|
|
100
|
|
|
101 1;
|
|
|
102
|
