comparison variant_effect_predictor/Bio/EnsEMBL/Variation/MotifFeatureVariation.pm @ 0:1f6dce3d34e0

Uploaded
author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:1f6dce3d34e0
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::MotifFeatureVariation;
22
23 use strict;
24 use warnings;
25
26 use Bio::EnsEMBL::Variation::MotifFeatureVariationAllele;
27 use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(overlap);
28
29 use base qw(Bio::EnsEMBL::Variation::RegulationVariation);
30
31 sub new {
32 my $class = shift;
33
34 my %args = @_;
35
36 # swap a '-motif_feature' argument for a '-feature' one for the superclass
37
38 for my $arg (keys %args) {
39 if (lc($arg) eq '-motif_feature') {
40 $args{'-feature'} = delete $args{$arg};
41 }
42 }
43
44 # call the superclass constructor
45 my $self = $class->SUPER::new(%args) || return undef;
46
47 # rebless the alleles from vfoas to mfvas
48 map { bless $_, 'Bio::EnsEMBL::Variation::MotifFeatureVariationAllele' }
49 @{ $self->get_all_MotifFeatureVariationAlleles };
50
51 return $self;
52 }
53
54 sub motif_feature_stable_id {
55 my $self = shift;
56 return $self->SUPER::feature_stable_id(@_);
57 }
58
59 sub motif_feature {
60 my ($self, $mf) = @_;
61 return $self->SUPER::feature($mf, 'MotifFeature');
62 }
63
64 sub add_MotifFeatureVariationAllele {
65 my $self = shift;
66 return $self->SUPER::add_VariationFeatureOverlapAllele(@_);
67 }
68
69 sub get_reference_MotifFeatureVariationAllele {
70 my $self = shift;
71 return $self->SUPER::get_reference_VariationFeatureOverlapAllele(@_);
72 }
73
74 sub get_all_alternate_MotifFeatureVariationAlleles {
75 my $self = shift;
76 return $self->SUPER::get_all_alternate_VariationFeatureOverlapAlleles(@_);
77 }
78
79 sub get_all_MotifFeatureVariationAlleles {
80 my $self = shift;
81 return $self->SUPER::get_all_VariationFeatureOverlapAlleles(@_);
82 }
83
84 sub _motif_feature_seq {
85 my $self = shift;
86
87 my $mf = $self->motif_feature;
88
89 my $mf_seq = $mf->{_variation_effect_feature_cache}->{seq} ||= $mf->seq;
90
91 return $mf_seq;
92 }
93
94 1;