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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 Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric - default Ensembl
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24 InternalIdMapper implementation for genes
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25
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26 =head1 SYNOPSIS
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27
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28 =head1 DESCRIPTION
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29
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30 =head1 METHODS
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31
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32 =cut
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33
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34 package Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric;
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35
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36 use strict;
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37 use warnings;
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38 no warnings 'uninitialized';
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39
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40 use Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper;
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41 our @ISA = qw(Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper);
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42
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43 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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44 use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
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45
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46
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47 #
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48 # basic mapping
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49 #
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50 sub init_basic {
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51 my $self = shift;
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52 my $num = shift;
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53 my $gsb = shift;
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54 my $mappings = shift;
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55 my $gene_scores = shift;
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56
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57 $self->logger->info("Basic gene mapping...\n", 0, 'stamped');
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58
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59 $mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
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60 $num++;
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61 my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $mappings,
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62 "gene_matrix$num");
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63
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64 return ($new_scores, $mappings);
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65 }
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66
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67
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68 #
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69 # build the synteny from unambiguous mappings
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70 #
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71 sub synteny {
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72 my $self = shift;
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73 my $num = shift;
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74 my $gsb = shift;
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75 my $mappings = shift;
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76 my $gene_scores = shift;
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77
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78 unless ($gene_scores->loaded) {
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79 $self->logger->info("Synteny Framework building...\n", 0, 'stamped');
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80 my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
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81 my $sf = Bio::EnsEMBL::IdMapping::SyntenyFramework->new(
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82 -DUMP_PATH => $dump_path,
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83 -CACHE_FILE => 'synteny_framework.ser',
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84 -LOGGER => $self->logger,
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85 -CONF => $self->conf,
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86 -CACHE => $self->cache,
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87 );
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88 $sf->build_synteny($mappings);
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89
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90 # use it to rescore the genes
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91 $self->logger->info("\nSynteny assisted mapping...\n", 0, 'stamped');
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92 $gene_scores = $sf->rescore_gene_matrix_lsf($gene_scores);
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93
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94 # checkpoint
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95 $gene_scores->write_to_file;
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96 }
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97
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98 my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
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99 $num++;
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100 my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
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101 "gene_matrix$num");
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102
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103 return ($new_scores, $new_mappings);
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104 }
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105
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106
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107 #
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108 # rescore with simple scoring function and try again
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109 #
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110 sub best_transcript {
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111 my $self = shift;
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112 my $num = shift;
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113 my $gsb = shift;
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114 my $mappings = shift;
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115 my $gene_scores = shift;
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116 my $transcript_scores = shift;
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117
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118 $self->logger->info("Retry with simple best transcript score...\n", 0, 'stamped');
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119
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120 unless ($gene_scores->loaded) {
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121 $gsb->simple_gene_rescore($gene_scores, $transcript_scores);
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122 $gene_scores->write_to_file;
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123 }
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124
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125 my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
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126 $num++;
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127 my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
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128 "gene_matrix$num");
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129
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130 return ($new_scores, $new_mappings);
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131 }
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132
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133
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134 #
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135 # rescore by penalising scores between genes with different biotypes
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136 #
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137 sub biotype {
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138 my $self = shift;
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139 my $num = shift;
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140 my $gsb = shift;
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141 my $mappings = shift;
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142 my $gene_scores = shift;
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143
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144 $self->logger->info("Retry with biotype disambiguation...\n", 0, 'stamped');
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145
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146 unless ($gene_scores->loaded) {
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147 $gsb->biotype_gene_rescore($gene_scores);
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148 $gene_scores->write_to_file;
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149 }
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150
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151 my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
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152 $num++;
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153 my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
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154 "gene_matrix$num");
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155
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156 return ($new_scores, $new_mappings);
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157 }
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158
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159
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160 #
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161 # selectively rescore by penalising scores between genes with different
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162 # internalIDs
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163 #
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164 sub internal_id {
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165 my $self = shift;
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166 my $num = shift;
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167 my $gsb = shift;
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168 my $mappings = shift;
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169 my $gene_scores = shift;
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170
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171 $self->logger->info("Retry with internalID disambiguation...\n", 0, 'stamped');
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172
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173 unless ($gene_scores->loaded) {
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174 $gsb->internal_id_rescore($gene_scores);
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175 $gene_scores->write_to_file;
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176 }
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177
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178 my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
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179 $num++;
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180 my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
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181 "gene_matrix$num");
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182
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183 return ($new_scores, $new_mappings);
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184 }
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185
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186
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187 1;
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188
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