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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::BaseStructuralVariation
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22 #
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23 # Copyright (c) 2011 Ensembl
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24 #
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25
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26
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27 =head1 NAME
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28
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29 Bio::EnsEMBL::Variation::BaseStructuralVariation - Ensembl representation of a structural variant.
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30
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31 =head1 SYNOPSIS
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32
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33 # Structural variation representing a CNV
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34 $sv = Bio::EnsEMBL::Variation::StructuralVariation->new
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35 (-variation_name => 'esv25480',
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36 -class_so_term => 'structural_variant',
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37 -source => 'DGVa',
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38 -source_description => 'Database of Genomic Variants Archive',
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39 -study_name => 'estd20',
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40 -study_description => 'Conrad 2009 "Origins and functional impact of copy number variation in the human genome." PMID:19812545 [remapped from build NCBI36]',
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41 -study_url => 'ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd20_Conrad_et_al_2009',
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42 -external_reference => 'pubmed/19812545');
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43
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44 ...
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45
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46 print $sv->name(), ":", $sv->var_class();
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47
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48 =head1 DESCRIPTION
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49
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50 This is a class representing a structural variation from the
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51 ensembl-variation database. A structural variant may have a copy number variation, a tandem duplication,
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52 an inversion of the sequence or others structural variations.
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53
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54 The position of a StructuralVariation object on the Genome is represented
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55 by the B<Bio::EnsEMBL::Variation::StructuralVariationFeature> class.
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56
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57 =head1 METHODS
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58
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59 =cut
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60
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61 use strict;
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62 use warnings;
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63
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64 package Bio::EnsEMBL::Variation::BaseStructuralVariation;
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65
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66 use Bio::EnsEMBL::Storable;
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67 use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
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68 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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69 use Bio::EnsEMBL::Variation::Utils::Constants qw(%VARIATION_CLASSES);
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70 use Bio::EnsEMBL::Variation::Failable;
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71 our @ISA = ('Bio::EnsEMBL::Storable','Bio::EnsEMBL::Variation::Failable');
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72
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73 =head2 new
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74
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75 Arg [-dbID] :
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76 see superclass constructor
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77
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78 Arg [-ADAPTOR] :
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79 see superclass constructor
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80
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81 Arg [-VARIATION_NAME] :
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82 string - the name of the structural variant.
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83
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84 Arg [-CLASS_SO_TERM] :
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85 string - the sequence ontology term defining the class of the structural variant.
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86
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87 Arg [-SOURCE] :
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88 string - the name of the source where the structural variant comes from
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89
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90 Arg [-SOURCE_DESCRIPTION] :
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91 string - description of the source
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92
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93 Arg [-TYPE] :
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94 string - the class of structural variant e.g. 'copy_number_variation'
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95
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96 Arg [-STUDY] :
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97 object ref - the study object describing where the structural variant comes from.
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98
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99 Arg [-VALIDATION_STATUS] :
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100 string - the status of the structural variant (e.g. validated, not validated, ...)
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101
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102 Arg [-IS_EVIDENCE] :
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103 int - flag to inform whether the structural variant is a supporting evidence (1) or not (0).
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104
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105 Arg [-IS_SOMATIC] :
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106 int - flag to inform whether the structural variant is a somatic (1) or germline (0).
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107
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108 Example for a structural variation:
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109 $sv = Bio::EnsEMBL::Variation::StructuralVariation->new
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110 (-variation_name => 'esv25480',
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111 -class_so_term => 'copy_number_variation',
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112 -source => 'DGVa',
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113 -source_description => 'Database of Genomic Variants Archive',
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114
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115 Description: Constructor. Instantiates a new structural variant object.
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116 Returntype : Bio::EnsEMBL::Variation::StructuralVariation or
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117 Bio::EnsEMBL::Variation::SupportingStructuralVariation
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118 Exceptions : none
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119 Caller : general
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120 Status : At Risk
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121
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122 =cut
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123
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124 sub new {
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125 my $caller = shift;
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126 my $class = ref($caller) || $caller;
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127
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128 my (
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129 $dbID,
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130 $adaptor,
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131 $var_name,
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132 $source,
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133 $source_version,
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134 $source_description,
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135 $class_so_term,
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136 $study,
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137 $validation_status,
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138 $is_evidence,
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139 $is_somatic
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140 ) = rearrange([qw(
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141 dbID
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142 ADAPTOR
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143 VARIATION_NAME
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144 SOURCE
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145 SOURCE_VERSION
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146 SOURCE_DESCRIPTION
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147 CLASS_SO_TERM
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148 STUDY
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149 VALIDATION_STATES
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150 IS_EVIDENCE
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151 IS_SOMATIC
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152 )], @_);
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153
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154 my $self = bless {
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155 'dbID' => $dbID,
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156 'adaptor' => $adaptor,
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157 'variation_name' => $var_name,
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158 'source' => $source,
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159 'source_version' => $source_version,
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160 'source_description' => $source_description,
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161 'class_SO_term' => $class_so_term,
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162 'study' => $study,
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163 'validation_status' => $validation_status,
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164 'is_evidence' => $is_evidence || 0,
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165 'is_somatic' => $is_somatic || 0,
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166 };
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167 return $self;
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168 }
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169
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170
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171
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172 sub new_fast {
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173 my $class = shift;
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174 my $hashref = shift;
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175 return bless $hashref, $class;
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176 }
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177
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178
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179 =head2 display_id
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180
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181 Arg [1] : none
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182 Example : print $sv->display_id(), "\n";
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183 Description: Returns the 'display' identifier for this structural variant.
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184 Returntype : string
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185 Exceptions : none
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186 Caller : webcode
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187 Status : At Risk
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188
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189 =cut
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190
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191 sub display_id {
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192 my $self = shift;
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193 return $self->{'variation_name'} || '';
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194 }
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195
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196
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197
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198 =head2 variation_name
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199
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200 Arg [1] : string $newval (optional)
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201 The new value to set the variation_name attribute to
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202 Example : $variation_name = $obj->variation_name()
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203 Description: Getter/Setter for the variation_name attribute. This is the
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204 name of the variation associated with this feature.
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205 Returntype : string
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206 Exceptions : none
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207 Caller : general
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208 Status : Stable
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209
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210 =cut
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211
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212 sub variation_name{
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213 my $self = shift;
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214 return $self->{'variation_name'} = shift if(@_);
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215 return $self->{'variation_name'};
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216 }
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217
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218 =head2 var_class
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219
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220 Args : None
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221 Example : my $sv_class = $sv->var_class()
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222 Description : Getter/setter for the class of structural variant
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223 ReturnType : String
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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 var_class {
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231 my $self = shift;
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232
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233 unless ($self->{class_display_term}) {
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234 my $display_term = $VARIATION_CLASSES{$self->{class_SO_term}}->{display_term};
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235
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236 warn "No display term for SO term: ".$self->{class_SO_term} unless $display_term;
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237
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238 $self->{class_display_term} = $display_term || $self->{class_SO_term};
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239 }
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240
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241 return $self->{class_display_term};
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242 }
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243
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244
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245 =head2 class_SO_term
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246
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247 Args : None
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248 Example : my $sv_so_term = $svf->class_SO_term()
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249 Description : Getter for the class of structural variant, returning the SO term
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250 ReturnType : String
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251 Exceptions : none
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252 Caller : General
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253 Status : At Risk
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254
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255 =cut
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256
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257 sub class_SO_term {
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258 my $self = shift;
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259
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260 return $self->{class_SO_term};
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261 }
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262
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263
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264 =head2 source
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265
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266 Arg [1] : string $source (optional)
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267 The new value to set the source attribute to
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268 Example : $source = $svf->source()
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269 Description: Getter/Setter for the source attribute
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270 Returntype : string
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271 Exceptions : none
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272 Caller : general
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273 Status : At Risk
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274
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275 =cut
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276
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277 sub source {
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278 my $self = shift;
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279 return $self->{'source'} = shift if(@_);
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280 return $self->{'source'};
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281 }
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282
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283
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284 =head2 source_version
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285
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286 Arg [1] : string $source_version (optional)
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287 The new value to set the source_version attribute to
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288 Example : $source_version = $svf->source_version()
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289 Description: Getter/Setter for the source_version attribute
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290 Returntype : string
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291 Exceptions : none
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292 Caller : general
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293 Status : At Risk
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294
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295 =cut
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296
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297 sub source_version {
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298 my $self = shift;
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299 return $self->{'source_version'} = shift if(@_);
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300 return $self->{'source_version'};
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301 }
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302
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303
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304 =head2 source_description
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305
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306 Arg [1] : string $source_description (optional)
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307 The new value to set the source_description attribute to
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308 Example : $source_description = $svf->source_description()
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309 Description: Getter/Setter for the source_description attribute
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310 Returntype : string
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311 Exceptions : none
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312 Caller : general
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313 Status : At Risk
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314
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315 =cut
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316
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317 sub source_description {
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318 my $self = shift;
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319 return $self->{'source_description'} = shift if(@_);
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320 return $self->{'source_description'};
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321 }
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322
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323
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324 =head2 get_all_validation_states
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325
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326 Arg [1] : none
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327 Example : my @vstates = @{$v->get_all_validation_states()};
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328 Description: Retrieves all validation states for this structural variation. Current
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329 possible validation statuses are 'validated','not validated',
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330 'high quality'
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331 Returntype : reference to list of strings
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332 Exceptions : none
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333 Caller : general
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334 Status : At Risk
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335
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336 =cut
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337
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338 sub get_all_validation_states {
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339 my $self = shift;
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340
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341 return $self->{'validation_status'} || [];
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342 }
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343
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344
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345 =head2 is_evidence
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346
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347 Arg [1] : int $flag (optional)
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348 Example : $is_evidence = $obj->is_evidence()
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349 Description: Getter/Setter of a flag to inform whether the structural variant is a
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350 supporting evidence (1) or not (0).
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351 Returntype : int
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352 Exceptions : none
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353 Caller : general
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354 Status : Stable
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355
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356 =cut
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357
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358 sub is_evidence{
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359 my $self = shift;
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360 return $self->{'is_evidence'} = shift if(@_);
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361 return $self->{'is_evidence'};
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362 }
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363
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364 =head2 is_somatic
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365
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366 Arg [1] : int $flag (optional)
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367 Example : $is_somatic = $obj->is_somatic()
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368 Description: Getter/Setter of a flag to inform whether the structural variant is somatic (1) or germline (0).
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369 Returntype : int
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370 Exceptions : none
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371 Caller : general
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372 Status : Stable
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373
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374 =cut
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375
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376 sub is_somatic{
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377 my $self = shift;
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378 return $self->{'is_somatic'} = shift if(@_);
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379 return $self->{'is_somatic'};
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380 }
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381
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382
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383 =head2 study
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384
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385 Arg [1] : Bio::EnsEMBL::Variation::Study (optional)
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386 Example : $study = $sv->study()
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387 Description: Getter/Setter for the study object
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388 Returntype : Bio::EnsEMBL::Variation::Study
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389 Exceptions : none
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390 Caller : general
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391 Status : At Risk
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392
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393 =cut
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394
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395 sub study {
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396 my $self = shift;
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397 return $self->{'study'} = shift if(@_);
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398 return $self->{'study'};
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399 }
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400
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401
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402 =head2 study_name
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403
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404 Arg [1] : string $study (optional)
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405 The new value to set the study attribute to
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406 Example : $study = $sv->study()
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407 Description: Getter/Setter for the study attribute
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408 Returntype : string
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409 Exceptions : none
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410 Caller : general
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411 Status : Deprecated
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412
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413 =cut
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414
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415 sub study_name {
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416 my $self = shift;
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417 deprecate('Use the method "study" instead (returns a Bio::EnsEMBL::Variation::Study object).');
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418 return undef if (!$self->study);
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419 return $self->study->name = shift if(@_);
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420 return $self->study->name;
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421 }
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422
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423
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424
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425 =head2 study_description
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426
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427 Arg [1] : string $study_description (optional)
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428 The new value to set the study_description attribute to
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429 Example : $study_description = $sv->study_description()
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430 Description: Getter/Setter for the study_description attribute
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431 Returntype : string
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432 Exceptions : none
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433 Caller : general
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434 Status : Deprecated
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435
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436 =cut
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437
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438 sub study_description {
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439 my $self = shift;
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440 deprecate('Use the method "study" instead (returns a Bio::EnsEMBL::Variation::Study object).');
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441 return undef if (!$self->study);
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442 return $self->study->description = shift if(@_);
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443 return $self->study->description;
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444 }
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445
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446 =head2 study_url
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447
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448 Arg [1] : string $newval (optional)
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449 The new value to set the study_url attribute to
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450 Example : $paper = $obj->study_url()
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451 Description: Getter/Setter for the study_url attribute.This is the link to the website where the data are stored.
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452 Returntype : string
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453 Exceptions : none
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454 Caller : general
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455 Status : Deprecated
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456
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457 =cut
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458
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459 sub study_url{
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460 my $self = shift;
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461 deprecate('Use the method "study" instead (returns a Bio::EnsEMBL::Variation::Study object).');
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462 return undef if (!$self->study);
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463 return $self->study->url = shift if(@_);
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464 return $self->study->url;
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465 }
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466
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467
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468 =head2 external_reference
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469
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470 Arg [1] : string $newval (optional)
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471 The new value to set the external reference attribute to
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472 Example : $paper = $obj->external_reference()
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473 Description: Getter/Setter for the external reference attribute. This is the
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474 pubmed/id or project name associated with this study.
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475 Returntype : string
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476 Exceptions : none
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477 Caller : general
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478 Status : Deprecated
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479
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480 =cut
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481
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482 sub external_reference{
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483 my $self = shift;
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484 deprecate('Use the method "study" instead (returns a Bio::EnsEMBL::Variation::Study object).');
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485 return undef if (!$self->study);
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486 return $self->study->external_reference = shift if(@_);
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487 return $self->study->external_reference;
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488 }
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489
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490
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491 =head2 get_all_StructuralVariationFeatures
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492
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493 Args : None
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494 Example : $svfs = $sv->get_all_StructuralVariationFeatures();
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495 Description : Retrieves all StructuralVariationFeature for this structural variant
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496 ReturnType : reference to list of Bio::EnsEMBL::Variation::StructuralVariationFeature
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497 Exceptions : None
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498 Caller : general
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499 Status : At Risk
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500
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501 =cut
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502
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503 sub get_all_StructuralVariationFeatures{
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504 my $self = shift;
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505
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506 if(defined $self->{'adaptor'}) {
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507
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508 # get structural variation feature adaptor
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509 my $svf_adaptor = $self->{'adaptor'}->db()->get_StructuralVariationFeatureAdaptor();
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510
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511 return $svf_adaptor->fetch_all_by_StructuralVariation($self);
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512 }
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513 else {
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514 warn("No variation database attached");
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515 return [];
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516 }
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517 }
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518
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519
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520 =head2 get_all_StructuralVariationAnnotations
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521
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522 Args : None
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523 Example : $svas = $sv->get_all_StructuralVariationAnnotations();
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524 Description : Retrieves all get_all_StructuralVariationAnnotation for this structural variant
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525 ReturnType : reference to list of Bio::EnsEMBL::Variation::StructuralVariationAnnotation
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526 Exceptions : None
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527 Caller : general
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528 Status : At Risk
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529
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530 =cut
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531
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532 sub get_all_StructuralVariationAnnotations{
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533 my $self = shift;
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534
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535 if(defined $self->{'adaptor'}) {
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536
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537 # get structural variation annotation adaptor
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538 my $sva_adaptor = $self->{'adaptor'}->db()->get_StructuralVariationAnnotationAdaptor();
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539
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540 return $sva_adaptor->fetch_all_by_StructuralVariation($self);
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541 }
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542 else {
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543 warn("No variation database attached");
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544 return [];
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545 }
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546 }
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547
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548
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549 =head2 summary_as_hash
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550
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551 Example : $sv_summary = $sv->summary_as_hash();
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552 Description : Retrieves a textual summary of this StructuralVariation object.
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553 Returns : hashref of descriptive strings
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554
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555 =cut
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556
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557 sub summary_as_hash {
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558 my $self = shift;
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559 my %summary;
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560 $summary{'display_id'} = $self->display_id;
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561 $summary{'study_name'} = $self->study_name;
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562 $summary{'study_description'} = $self->study_description;
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563 $summary{'class'} = $self->var_class;
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564 return \%summary;
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565
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566 }
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567
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568 1;
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