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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 # Ensembl module for Bio::EnsEMBL::Variation::VariationSet
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22 #
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23 # Copyright (c) 2010 Ensembl
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24 #
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25
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26 =head1 NAME
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27
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28 Bio::EnsEMBL::Variation::VariationSet - Ensembl representation of a set of
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29 variations.
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30
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31 =head1 SYNOPSIS
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32
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33 use Bio::EnsEMBL::Variation::VariationSet;
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34
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35 ...
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36
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37
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38
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39 =head1 DESCRIPTION
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40
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41 This is a class representing a set of variations that are grouped by e.g.
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42 study, method, quality measure etc.
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43
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44 =head1 METHODS
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45
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46 =cut
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47
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48
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49 use strict;
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50 use warnings;
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51
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52 package Bio::EnsEMBL::Variation::VariationSet;
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53
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54 use Bio::EnsEMBL::Storable;
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55 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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56 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
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57 use Bio::EnsEMBL::Utils::Iterator;
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58
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59 use vars qw(@ISA);
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60
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61 @ISA = qw(Bio::EnsEMBL::Storable);
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62
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63
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64 =head2 new
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65
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66 Arg [dbID] :
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67 int - unique internal identifier for this allele group
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68
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69 Arg [ADAPTOR] :
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70 Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor
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71
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72 Arg [NAME] :
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73 string - the name of this variation set
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74
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75 Arg [DESCRIPTION] :
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76 string - A description explaining the charcteristics of this variation set
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77
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78 Arg [SHORT_NAME] :
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79 string - the short name of this variation set
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80
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81 Example :
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82 $ag = Bio::EnsEMBL::Variation::VariationSet->new
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83 (
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84 -dbID => 12,
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85 -adaptor => $var_set_adaptor,
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86 -name => 'Phenotype-associated variations',
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87 -description => 'Variations that have been associated with a phenotype',
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88 -short_name => 'ph_variants'
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89 );
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90 Description: Constructor. Instantiates a new VariationSet
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91 Returntype : Bio::EnsEMBL::Variation::VariationSet
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92 Exceptions : none
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93 Caller : general
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94 Status : At Risk
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95
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96 =cut
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97
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98 sub new {
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99 my $class = shift;
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100
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101 my ($dbID, $adaptor, $name, $description, $short_name) =
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102 rearrange([qw(DBID ADAPTOR NAME DESCRIPTION SHORT_NAME)], @_);
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103
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104 # Check that the dbID does not exceed the maximum dbID that can be stored in the variation_set_id SET construct in variation_set_variation
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105 warn("Primary key variation_set_id $dbID for variation set '$name' exceeds " . $Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::MAX_VARIATION_SET_ID . ". Therefore, this variation set cannot be properly referenced in variation_set_variation") if ($dbID > $Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::MAX_VARIATION_SET_ID);
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106
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107 return bless {'dbID' => $dbID,
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108 'adaptor' => $adaptor,
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109 'name' => $name,
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110 'description' => $description,
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111 'short_name' => $short_name}, $class;
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112 }
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113
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114 =head2 description
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115
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116 Arg [1] : string $description
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117 Example : print $vs->description();
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118 Description: Getter/Setter for the description of this VariationSet
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119 Returntype : string
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120 Exceptions : none
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121 Caller : general
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122 Status : At Risk
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123
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124 =cut
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125
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126 sub description {
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127 my $self = shift;
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128 my $desc = shift;
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129
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130 $self->{'description'} = $desc if (defined($desc));
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131
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132 return $self->{'description'};
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133 }
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134
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135 =head2 get_all_sub_VariationSets
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136 Arg [1] : (optional) boolean $only_immediate
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137 If true, will only get the direct subsets of this variation. The default behaviour is
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138 to recursively get all subsets.
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139 Example : print $vs->get_all_sub_VariationSets();
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140 Description: Recursively gets all variation sets that are subsets of this variation set.
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141 Returntype : reference to list of Bio::EnsEMBL::Variation::VariationSet
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142 Exceptions : none
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143 Caller : general
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144 Status : At Risk
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145
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146 =cut
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147
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148 sub get_all_sub_VariationSets {
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149 my $self = shift;
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150 my $only_immediate = shift;
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151
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152 # A database adaptor must be attached to this object
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153 if(!$self->adaptor()) {
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154 warning('Cannot get sub variation sets without attached adaptor');
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155 return [];
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156 }
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157
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158 return $self->adaptor->fetch_all_by_super_VariationSet($self,$only_immediate);
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159 }
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160
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161 =head2 get_all_super_VariationSets
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162 Arg [1] : (optional) boolean $only_immediate
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163 If true, will only get the direct supersets of this variation. The default behaviour is
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164 to recursively get all supersets.
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165 Example : print $vs->get_all_super_VariationSets();
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166 Description: Recursively gets all variation sets that are above this variation set.
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167 Returntype : reference to list of Bio::EnsEMBL::Variation::VariationSet
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168 Exceptions : none
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169 Caller : general
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170 Status : At Risk
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171
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172 =cut
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173
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174 sub get_all_super_VariationSets {
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175 my $self = shift;
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176 my $only_immediate = shift;
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177
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178 # A database adaptor must be attached to this object
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179 if(!$self->adaptor()) {
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180 warning('Cannot get super variation sets without attached adaptor');
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181 return [];
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182 }
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183
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184 return $self->adaptor->fetch_all_by_sub_VariationSet($self,$only_immediate);
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185 }
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186
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187 =head2 get_all_Variations
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188
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189 Example : print $vs->get_all_Variations();
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190 Description: Gets all variations belonging to this variation set and all of its subsets.
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191 Returntype : reference to list of Bio::EnsEMBL::Variation::Variation
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192 Exceptions : none
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193 Caller : general
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194 Status : At Risk
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195
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196 =cut
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197
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198 sub get_all_Variations {
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199 my $self = shift;
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200
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201 # A database adaptor must be attached to this object
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202 if(!$self->adaptor()) {
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203 warning('Cannot get variations without attached adaptor');
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204 return [];
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205 }
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206
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207 # Call the method in VariationAdaptor that will handle this
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208 my $variation_adaptor = $self->adaptor->db->get_VariationAdaptor();
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209 if(!$variation_adaptor) {
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210 warning('Could not get variation adaptor from database');
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211 return [];
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212 }
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213
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214 # Get all variations from this set (and its subsets)
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215 return $variation_adaptor->fetch_all_by_VariationSet($self);
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216 }
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217
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218
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219 =head2 get_all_StructuralVariations
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220
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221 Example : print $vs->get_all_StructuralVariations();
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222 Description: Gets all structural variations belonging to this variation set and all of its subsets.
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223 Returntype : reference to list of Bio::EnsEMBL::Variation::StructuralVariation
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224 Exceptions : none
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225 Caller : general
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226 Status : At Risk
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227
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228 =cut
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229
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230 sub get_all_StructuralVariations {
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231 my $self = shift;
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232
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233 # A database adaptor must be attached to this object
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234 if(!$self->adaptor()) {
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235 warning('Cannot get structural variations without attached adaptor');
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236 return [];
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237 }
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238
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239 # Call the method in StructuralVariationAdaptor that will handle this
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240 my $sv_adaptor = $self->adaptor->db->get_StructuralVariationAdaptor();
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241 if(!$sv_adaptor) {
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242 warning('Could not get structural variation adaptor from database');
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243 return [];
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244 }
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245
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246 # Get all variations from this set (and its subsets)
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247 return $sv_adaptor->fetch_all_by_VariationSet($self);
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248 }
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249
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250
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251 =head2 get_Variation_Iterator
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252
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253 Example : my $var_iterator = $vs->get_Variation_Iterator;
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254 Description: Gets an iterator over all variations belonging to this
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255 variation set and all of its subsets.
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256 Returntype : Bio::EnsEMBL::Utils::Iterator
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257 Exceptions : none
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258 Caller : general
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259 Status : Experimental
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260
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261 =cut
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262
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263 sub get_Variation_Iterator {
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264 my $self = shift;
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265
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266 # A database adaptor must be attached to this object
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267 unless ($self->adaptor) {
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268 warning('Cannot get variations without attached adaptor');
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269 return Bio::EnsEMBL::Utils::Iterator->new;
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270 }
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271
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272 # Call the method in VariationAdaptor that will handle this
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273 my $variation_adaptor = $self->adaptor->db->get_VariationAdaptor();
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274
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275 unless ($variation_adaptor) {
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276 warning('Could not get variation adaptor from database');
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277 return Bio::EnsEMBL::Utils::Iterator->new;
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278 }
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279
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280 # Get an iterator over variations from this set (and its subsets)
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281 return $variation_adaptor->fetch_Iterator_by_VariationSet($self);
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282 }
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283
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284
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285 =head2 get_StructuralVariation_Iterator
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286
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287 Example : my $sv_iterator = $vs->get_StructuralVariation_Iterator;
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288 Description: Gets an iterator over all structural variations belonging to this
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289 variation set and all of its subsets.
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290 Returntype : Bio::EnsEMBL::Utils::Iterator
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291 Exceptions : none
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292 Caller : general
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293 Status : Experimental
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294
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295 =cut
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296
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297 sub get_StructuralVariation_Iterator {
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298 my $self = shift;
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299
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300 # A database adaptor must be attached to this object
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301 unless ($self->adaptor) {
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302 warning('Cannot get structural variations without attached adaptor');
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303 return Bio::EnsEMBL::Utils::Iterator->new;
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304 }
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305
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306 # Call the method in StructuralVariationAdaptor that will handle this
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307 my $sv_adaptor = $self->adaptor->db->get_StructuralVariationAdaptor();
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308
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309 unless ($sv_adaptor) {
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310 warning('Could not get dructural variation adaptor from database');
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311 return Bio::EnsEMBL::Utils::Iterator->new;
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312 }
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313
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314 # Get an iterator over Structural variations from this set (and its subsets)
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315 return $sv_adaptor->fetch_Iterator_by_VariationSet($self);
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316 }
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317
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318
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319 =head2 get_all_VariationFeatures_by_Slice
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320
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321 Arg [1] : Bio::EnsEMBL:Variation::Slice $slice
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322 Example : my @vfs =
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323 @{$vs->get_all_VariationFeatures_by_Slice($slice)};
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324 Description: Retrieves all variation features in a slice that belong to
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325 this set.
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326 Returntype : reference to list Bio::EnsEMBL::Variation::VariationFeature
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327 Exceptions : throw on bad argument
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328 Caller : general
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329 Status : Stable
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330
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331 =cut
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332
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333 sub get_all_VariationFeatures_by_Slice {
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334 my $self = shift;
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335 my $slice = shift;
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336
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337 if(!$self->adaptor()) {
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338 warning('Cannot get variation features without attached adaptor');
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339 return [];
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340 }
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341
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342 my $vfa = $self->adaptor->db->get_VariationFeatureAdaptor();
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343 if(!$vfa) {
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344 warning('Could not get variation feature adaptor from database');
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345 return [];
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346 }
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347 return $vfa->fetch_all_by_Slice_VariationSet($slice,$self);
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348 }
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349
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350 =head2 name
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351
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352 Arg [1] : string $name
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353 Example : print $vs->name();
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354 Description: Getter/Setter for the name of this VariationSet
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355 Returntype : string
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356 Exceptions : none
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357 Caller : general
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358 Status : At Risk
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359
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360 =cut
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361
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362 sub name {
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363 my $self = shift;
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364 my $name = shift;
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365
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366 $self->{'name'} = $name if (defined($name));
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367
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368 return $self->{'name'};
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369 }
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370
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371 =head2 short_name
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372
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373 Arg [1] : string $short_name
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374 Example : print $vs->short_name();
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375 Description: Getter/Setter for the short name of this VariationSet
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376 Returntype : string
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377 Exceptions : none
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378 Caller : general
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379
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380 =cut
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381
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382 sub short_name {
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383 my $self = shift;
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384 my $short_name = shift;
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385
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386 $self->{'short_name'} = $short_name if (defined($short_name));
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387
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388 return $self->{'short_name'};
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389 }
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390
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391 # API-internal subroutine to get the bitvalue of this set's id and all of its subsets (unless specifically indicated not to)
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392 sub _get_bitvalue {
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393 my $self = shift;
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394 my @args = @_;
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395
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396 # If the subsets should be exluded, call the subroutine in the adaptor and return the result. No caching.
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397 if (@args) {
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398 return $self->adaptor->_get_bitvalue($self,@args);
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399 }
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400
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401 # Check if we have cached the bitvalue (including subsets), otherwise get it and cache it
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402 unless (exists($self->{'_bitvalue'})) {
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403 $self->{'_bitvalue'} = $self->adaptor->_get_bitvalue($self);
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404 }
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405
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406 # Return the cached value
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407 return $self->{'_bitvalue'};
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408 }
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409
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410 1;
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