|
0
|
1 =head1 LICENSE
|
|
|
2
|
|
|
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
|
|
|
4 Genome Research Limited. All rights reserved.
|
|
|
5
|
|
|
6 This software is distributed under a modified Apache license.
|
|
|
7 For license details, please see
|
|
|
8
|
|
|
9 http://www.ensembl.org/info/about/code_licence.html
|
|
|
10
|
|
|
11 =head1 CONTACT
|
|
|
12
|
|
|
13 Please email comments or questions to the public Ensembl
|
|
|
14 developers list at <dev@ensembl.org>.
|
|
|
15
|
|
|
16 Questions may also be sent to the Ensembl help desk at
|
|
|
17 <helpdesk@ensembl.org>.
|
|
|
18
|
|
|
19 =cut
|
|
|
20
|
|
|
21 package Bio::EnsEMBL::Variation::Pipeline::BaseVariationProcess;
|
|
|
22
|
|
|
23 use strict;
|
|
|
24 use warnings;
|
|
|
25
|
|
|
26 use Bio::EnsEMBL::Variation::Pipeline::TranscriptFileAdaptor;
|
|
|
27
|
|
|
28 use Bio::EnsEMBL::Hive::AnalysisJob;
|
|
|
29
|
|
|
30 use base qw(Bio::EnsEMBL::Hive::Process);
|
|
|
31
|
|
|
32 sub param {
|
|
|
33 my $self = shift;
|
|
|
34
|
|
|
35 unless ($self->input_job) {
|
|
|
36 # if we don't have an input job, add a dummy one (used when we're not
|
|
|
37 # running as part of a pipeline proper)
|
|
|
38 $self->input_job(Bio::EnsEMBL::Hive::AnalysisJob->new);
|
|
|
39 }
|
|
|
40
|
|
|
41 return $self->SUPER::param(@_);
|
|
|
42 }
|
|
|
43
|
|
|
44 sub required_param {
|
|
|
45 my $self = shift;
|
|
|
46 my $param_name = shift;
|
|
|
47
|
|
|
48 my $param_value = $self->param($param_name, @_);
|
|
|
49
|
|
|
50 die "$param_name is a required parameter" unless defined $param_value;
|
|
|
51
|
|
|
52 return $param_value;
|
|
|
53 }
|
|
|
54
|
|
|
55 sub get_transcript_file_adaptor {
|
|
|
56 my $self = shift;
|
|
|
57 my $transcripts = shift;
|
|
|
58
|
|
|
59 unless ($self->{tfa}) {
|
|
|
60 $self->{tfa} = Bio::EnsEMBL::Variation::Pipeline::TranscriptFileAdaptor->new(
|
|
|
61 fasta_file => $self->param('fasta_file'),
|
|
|
62 transcripts => $transcripts,
|
|
|
63 );
|
|
|
64 }
|
|
|
65
|
|
|
66 return $self->{tfa};
|
|
|
67 }
|
|
|
68
|
|
|
69 sub get_species_adaptor {
|
|
|
70 my ($self, $group) = @_;
|
|
|
71
|
|
|
72 my $species = $self->required_param('species');
|
|
|
73
|
|
|
74 return $self->get_adaptor($species, $group);
|
|
|
75 }
|
|
|
76
|
|
|
77 sub get_adaptor {
|
|
|
78 my ($self, $species, $group) = @_;
|
|
|
79
|
|
|
80 my $dba;
|
|
|
81
|
|
|
82 eval {
|
|
|
83 $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);
|
|
|
84 };
|
|
|
85
|
|
|
86 unless (defined $dba) {
|
|
|
87 $self->_load_registry();
|
|
|
88 $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);
|
|
|
89 }
|
|
|
90
|
|
|
91 unless (defined $dba) {
|
|
|
92 die "Failed to a get DBA for $species and group $group";
|
|
|
93 }
|
|
|
94
|
|
|
95 return $dba;
|
|
|
96 }
|
|
|
97
|
|
|
98 sub _load_registry {
|
|
|
99 my ($self) = @_;
|
|
|
100
|
|
|
101 my $reg_file = $self->required_param('ensembl_registry');
|
|
|
102
|
|
|
103 Bio::EnsEMBL::Registry->load_all($reg_file, 0, 1);
|
|
|
104
|
|
|
105 return;
|
|
|
106 }
|
|
|
107
|
|
|
108 1;
|
