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1 =head1 LICENSE
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2
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3 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
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4 Copyright [2016-2018] EMBL-European Bioinformatics Institute
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5
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6 Licensed under the Apache License, Version 2.0 (the "License");
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7 you may not use this file except in compliance with the License.
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8 You may obtain a copy of the License at
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9
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10 http://www.apache.org/licenses/LICENSE-2.0
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11
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12 Unless required by applicable law or agreed to in writing, software
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13 distributed under the License is distributed on an "AS IS" BASIS,
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14 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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15 See the License for the specific language governing permissions and
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16 limitations under the License.
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17
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18 =head1 CONTACT
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19
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20 Ensembl <http://www.ensembl.org/info/about/contact/index.html>
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21
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22 =cut
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23
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24 =head1 NAME
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25
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26 miRNA
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27
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28 =head1 SYNOPSIS
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29
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30 mv miRNA.pm ~/.vep/Plugins
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31 ./vep -i variations.vcf --plugin miRNA
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32
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33 =head1 DESCRIPTION
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34
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35 A VEP plugin that determines where in the secondary structure of a miRNA a
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36 variant falls.
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37
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38 =cut
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39
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40 package miRNA;
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41
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42 use strict;
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43 use warnings;
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44
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45 use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
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46
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47 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
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48
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49 sub feature_types {
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50 return ['Transcript'];
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51 }
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52
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53 sub get_header_info {
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54 my $self = shift;
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55 return {
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56 miRNA => 'SO term for miRNA component containing the variant'
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57 }
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58 }
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59
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60 sub run {
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61 my ($self, $tva) = @_;
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62
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63 my $tv = $tva->transcript_variation;
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64 my $tr = $tva->transcript;
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65
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66 # obviously this only works for *RNA transcripts
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67 return {} unless $tr->biotype =~ /RNA/;
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68
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69 # and it only works if the TV falls in the cDNA
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70 return {} unless $tv->cdna_start && $tv->cdna_end;
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71
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72 # get attribute if already cached
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73 my ($attrib) = @{$tr->get_all_Attributes('ncRNA')};
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74
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75 # bit of a cheat to get attrib if ncRNA attribute hasn't been cached
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76 if(!$attrib && defined($self->{config}->{ta})) {
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77 delete $tr->{attributes};
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78 $tr->{adaptor} = $self->{config}->{ta};
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79 ($attrib) = @{$tr->get_all_Attributes('ncRNA')};
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80 }
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81
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82 return {} unless $attrib;
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83
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84 # split out string to get coords and structure string
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85 my ($start, $end, $struct) = split /\s+|\:/, $attrib->value;
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86 return {} unless $struct && $struct =~ /[\(\.\)]+/;
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87
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88 # variant not in given structure?
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89 return { miRNA => 'None' } unless $tv->cdna_start <= $end && $tv->cdna_end >= $start;
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90
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91 # parse out structure
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92 my @struct;
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93 while($struct =~ m/([\.\(\)])([0-9]+)?/g) {
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94 my $num = $2 || 1;
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95 push @struct, $1 for(1..$num);
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96 }
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97
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98 # get struct element types overlapped by variant
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99 my %chars;
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100 for my $pos($tv->cdna_start..$tv->cdna_end) {
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101 $pos -= $start;
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102 next if $pos < 0 or $pos > scalar @struct;
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103 $chars{$struct[$pos]} = 1;
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104 }
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105
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106 # map element types to SO terms
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107 my %map = (
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108 '(' => 'miRNA_stem',
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109 ')' => 'miRNA_stem',
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110 '.' => 'miRNA_loop'
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111 );
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112
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113 return {
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114 miRNA => join(",", sort map {$map{$_}} keys %chars)
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115 };
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116 }
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117
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118 1;
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119
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