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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 =head1 SYNOPSIS
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24
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25 =head1 DESCRIPTION
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26
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27 =head1 METHODS
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28
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29 =cut
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30
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31 package Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric;
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32
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33 use strict;
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34 use warnings;
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35 no warnings 'uninitialized';
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36
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37 use Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper;
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38 our @ISA = qw(Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper);
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39
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40 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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41
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42
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43 #
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44 # basic mapping
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45 #
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46 sub init_basic {
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47 my $self = shift;
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48 my $num = shift;
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49 my $esb = shift;
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50 my $mappings = shift;
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51 my $exon_scores = shift;
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52
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53 $self->logger->info("Basic exon mapping...\n", 0, 'stamped');
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54
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55 $mappings = $self->basic_mapping($exon_scores, "exon_mappings$num");
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56 $num++;
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57 my $new_scores = $esb->create_shrinked_matrix($exon_scores, $mappings,
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58 "exon_matrix$num");
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59
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60 return ($new_scores, $mappings);
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61 }
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62
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63
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64 #
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65 # reduce score for mappings of exons which do not belong to mapped
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66 # transcripts
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67 #
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68 sub mapped_transcript {
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69 my $self = shift;
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70 my $num = shift;
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71 my $esb = shift;
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72 my $mappings = shift;
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73 my $exon_scores = shift;
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74
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75 $self->logger->info("Exons in mapped transcript...\n", 0, 'stamped');
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76
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77 unless ($exon_scores->loaded) {
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78 $esb->non_mapped_transcript_rescore($exon_scores, $mappings);
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79 $exon_scores->write_to_file;
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80 }
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81
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82 $mappings = $self->basic_mapping($exon_scores, "exon_mappings$num");
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83 $num++;
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84 my $new_scores = $esb->create_shrinked_matrix($exon_scores, $mappings,
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85 "exon_matrix$num");
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86
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87 return ($new_scores, $mappings);
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88 }
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89
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90
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91 #
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92 # selectively rescore by penalising scores between exons with
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93 # different internalIDs
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94 #
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95 sub internal_id {
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96 my $self = shift;
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97 my $num = shift;
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98 my $esb = shift;
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99 my $mappings = shift;
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100 my $exon_scores = shift;
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101
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102 $self->logger->info( "Retry with internalID disambiguation...\n",
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103 0, 'stamped' );
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104
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105 if ( !$exon_scores->loaded() ) {
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106 $esb->internal_id_rescore($exon_scores);
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107 $exon_scores->write_to_file();
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108 }
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109
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110 $mappings = $self->basic_mapping( $exon_scores, "exon_mappings$num" );
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111 $num++;
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112 my $new_scores =
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113 $esb->create_shrinked_matrix( $exon_scores, $mappings,
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114 "exon_matrix$num" );
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115
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116 return ( $new_scores, $mappings );
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117 }
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118
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119
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120 1;
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121
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