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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 package Bio::EnsEMBL::IndividualSliceFactory;
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22
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23 use strict;
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24 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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25 use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
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26 use Bio::EnsEMBL::Slice;
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27 use Bio::EnsEMBL::Mapper;
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28 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
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29 use Scalar::Util qw(weaken);
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30
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31 =head2 new
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32 =cut
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33
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34 sub new{
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35 my $caller = shift;
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36 my $class = ref($caller) || $caller;
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37
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38 #creates many IndividualSlice objects from the Population
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39
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40 my ($population_name, $coord_system, $start, $end, $strand, $seq_region_name, $seq_region_length, $adaptor) = rearrange(['POPULATION', 'COORD_SYSTEM','START','END','STRAND','SEQ_REGION_NAME','SEQ_REGION_LENGTH', 'ADAPTOR'],@_);
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41
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42 my $self = bless {
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43 population_name => $population_name,
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44 coord_system => $coord_system,
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45 start => $start,
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46 end => $end,
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47 strand => $strand,
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48 seq_region_name => $seq_region_name,
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49 seq_region_length => $seq_region_length},$class;
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50
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51 $self->adaptor($adaptor);
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52 return $self;
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53 }
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54
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55 sub adaptor {
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56 my $self = shift;
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57
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58 if(@_) {
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59 my $ad = shift;
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60 if($ad && (!ref($ad) || !$ad->isa('Bio::EnsEMBL::DBSQL::BaseAdaptor'))) {
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61 throw('Adaptor argument must be a Bio::EnsEMBL::DBSQL::BaseAdaptor');
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62 }
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63 weaken($self->{'adaptor'} = $ad);
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64 }
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65
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66 return $self->{'adaptor'}
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67 }
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68
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69 sub get_all_IndividualSlice{
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70 my $self = shift;
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71
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72 my $slice;
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73 if(!$self->adaptor) {
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74 warning('Cannot get IndividualSlice features without attached adaptor');
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75 return '';
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76 }
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77 my $variation_db = $self->adaptor->db->get_db_adaptor('variation');
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78
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79 unless($variation_db) {
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80 warning("Variation database must be attached to core database to " .
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81 "retrieve variation information" );
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82 return '';
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83 }
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84 #get the AlleleFeatures in the Population
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85 my $af_adaptor = $variation_db->get_AlleleFeatureAdaptor;
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86
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87 if( $af_adaptor ) {
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88 #set the adaptor to retrieve data from genotype table
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89 $af_adaptor->from_IndividualSlice(1);
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90 #get the Individual for the given strain
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91 my $population_adaptor = $variation_db->get_PopulationAdaptor;
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92 my $individual_adaptor = $variation_db->get_IndividualAdaptor;
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93 if ($population_adaptor && $individual_adaptor){
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94 $slice = Bio::EnsEMBL::Slice->new(-coord_system => $self->{'coord_system'},
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95 -start => $self->{'start'},
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96 -end => $self->{'end'},
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97 -strand => $self->{'strand'},
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98 -seq_region_name => $self->{'seq_region_name'},
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99 -seq_region_length => $self->{'seq_region_length'},
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100 -adaptor => $self->adaptor
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101 );
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102 my $population = $population_adaptor->fetch_by_name($self->{'population_name'});
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103 #check that there is such population in the database
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104 if (defined $population){
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105 #get all the AlleleFeatures in the $population and the Slice given
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106 my $allele_features = $af_adaptor->fetch_all_by_Slice($slice,$population);
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107 #get Individuals in the Population
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108 my $individuals = $individual_adaptor->fetch_all_by_Population($population);
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109 return $self->_rearrange_Individuals_Alleles($individuals,$allele_features);
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110 }
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111 else{
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112 warning("Population not in the database");
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113 return '';
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114
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115 }
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116 }
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117 else{
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118 warning("Not possible to retrieve PopulationAdaptor from the variation database");
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119 return '';
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120 }
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121 }
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122
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123 else{
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124 warning("Not possible to retrieve AlleleFeatureAdaptor from variation database");
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125 return '';
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126 }
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127 }
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128
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129 sub _rearrange_Individuals_Alleles{
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130 my $self = shift;
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131 my $individuals = shift;
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132 my $allele_features;
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133 my $individual_slice;
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134 #create the hash with all the individuals
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135 my %individuals_ids;
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136 #foreach of the individual, create the IndividualSlice object and add it to the mapping hash
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137 foreach my $individual (@{$individuals}){
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138 $individual_slice = Bio::EnsEMBL::Variation::IndividualSlice->new(
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139 -coord_system => $self->{'coord_system'},
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140 -start => $self->{'$start'},
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141 -end => $self->{'end'},
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142 -strand => $self->{'strand'},
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143 -seq_region_name => $self->{'seq_region_name'},
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144 -seq_region_length => $self->{'seq_region_length'},
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145 -individual => $individual->name);
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146
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147 $individuals_ids{$individual->dbID} = $individual_slice;
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148 }
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149
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150 #and rearrange all the AlleleFeatures to the individuals
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151 foreach my $allele_feature (@{$allele_features}){
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152 $individuals_ids{$allele_feature->{'_sample_id'}}->add_AlleleFeature($allele_feature);
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153 }
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154 my @result = values %individuals_ids;
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155 return \@result;
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156 }
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157
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158
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159 1;
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