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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::StructuralVariationAnnotation
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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::StructuralVariationAnnotation - Annotations for a structural variant (sample and phenotype annotations).
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30
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31 =head1 SYNOPSIS
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32
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33 $study = $study_adaptor->fetch_by_name('nstd37');
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34
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35 $sva = Bio::EnsEMBL::Variation::StructuralVariationAnnotation->new
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36 (-sample_name => 'ISCA_ID_5554',
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37 -clinical_significance => 'Not tested',
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38 -study => $study);
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39 ...
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40
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41 $sva->structural_variation->variation_name(),":", $sva->sample_name();
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42
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43 =head1 DESCRIPTION
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44
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45 This is a class representing the annotation of a structural variant
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46 from the ensembl-variation database. The actual structural variant information is
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47 represented by an associated Bio::EnsEMBL::Variation::StructuralVariation object.
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48
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49 =head1 METHODS
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50
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51 =cut
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52
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53 use strict;
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54 use warnings;
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55
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56 package Bio::EnsEMBL::Variation::StructuralVariationAnnotation;
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57
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58 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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59 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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60 use Bio::EnsEMBL::Variation::BaseStructuralVariation;
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61 use Bio::EnsEMBL::Storable;
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62 use Bio::EnsEMBL::Utils::Exception qw(deprecate);
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63
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64 use vars qw(@ISA);
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65
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66 @ISA = qw(Bio::EnsEMBL::Storable);
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67
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68 =head2 new
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69
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70 Arg [-dbID] :
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71 int - unique internal identifier for variation_annotation
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72
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73 Arg [-ADAPTOR] :
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74 Bio::EnsEMBL::Variation::DBSQL::StructuralVariationAnnotationAdaptor
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75 Adaptor which provides database connectivity for this StructuralVariationAnnotation object
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76
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77 Arg [-_PHENOTYPE_ID] :
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78 int _ the internal id of the phenotype
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79
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80 Arg [-PHENOTYPE_DESCRIPTION] :
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81 string - description of the phenotype
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82
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83 Arg [-SAMPLE_NAME] :
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84 string - name of the associated sample
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85
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86 Arg [-STRAIN_NAME] :
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87 string - name of the associated strain
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88
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89 Arg [-CLINICAL_SIGNIFICANCE] :
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90 string - clinical annotation for this structural variant.
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91
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92 Arg [-STUDY] :
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93 object ref - the study object describing where the annotated variation comes from.
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94
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95 Arg [_STRUCTURAL_VARIATION_ID] :
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96 int _ the internal id of the structural variant object associated with this
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97 identifier. TUsing this identifier the structural variant may be lazy-loaded from
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98 the database on demand.
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99
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100 Example :
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101 $study = $study_adaptor->fetch_by_name('nstd37');
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102
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103 $sva = Bio::EnsEMBL::Variation::StructuralVariationAnnotation->new
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104 (-sample_name => 'ISCA_ID_5554',
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105 -strain_name => 'ISCA',
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106 -clinical_significance => 'Not tested',
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107 -study => $study);
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108
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109 Description: Constructor. Instantiates a new StructuralVariationAnnotation object.
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110 Returntype : Bio::EnsEMBL::Variation::StructuralVariationAnnotation
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111 Exceptions : none
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112 Caller : general
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113 Status : At Risk
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114
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115 =cut
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116
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117 sub new {
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118 my $caller = shift;
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119 my $class = ref($caller) || $caller;
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120 my $self = $class->SUPER::new(@_);
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121
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122 my ($dbID,$adaptor,$phenotype_id,$phenotype_description,$structural_variation_id,$sample_name,
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123 $strain_name,$clinical_significance,$study) =
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124 rearrange([qw(dbID ADAPTOR _PHENOTYPE_ID PHENOTYPE_DESCRIPTION _STRUCTURAL_VARIATION_ID
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125 SAMPLE_NAME STRAIN_NAME CLINICAL_SIGNIFICANCE STUDY)],@_);
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126
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127 $self->{'dbID'} = $dbID;
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128 $self->{'adaptor'} = $adaptor;
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129 $self->{'_phenotype_id'} = $phenotype_id;
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130 $self->{'phenotype_description'} = $phenotype_description;
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131 $self->{'_structural_variation_id'} = $structural_variation_id;
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132 $self->{'sample_name'} = $sample_name;
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133 $self->{'strain_name'} = $strain_name;
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134 $self->{'clinical_significance'} = $clinical_significance;
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135 $self->{'study'} = $study;
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136 return $self;
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137 }
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138
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139
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140
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141 sub new_fast {
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142 my $class = shift;
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143 my $hashref = shift;
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144 return bless $hashref, $class;
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145 }
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146
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147
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148 =head2 structural_variation
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149
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150 Arg [1] : (optional) Bio::EnsEMBL::Variation::StructuralVariation or
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151 Bio::EnsEMBL::Variation::SupportingStructuralVariation $structural_variation
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152 Example : $sv = $svf->structural_variation();
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153 Description: Getter/Setter for the structural variant associated with this feature.
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154 If not set, and this StructuralVariationFeature has an associated adaptor
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155 an attempt will be made to lazy-load the structural variation from the
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156 database.
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157 Returntype : Bio::EnsEMBL::Variation::StructuralVariation or Bio::EnsEMBL::Variation::SupportingStructuralVariation
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158 Exceptions : throw on incorrect argument
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159 Caller : general
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160 Status : Stable
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161
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162 =cut
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163
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164 sub structural_variation {
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165 my $self = shift;
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166
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167 if(@_) {
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168 if(!ref($_[0]) || (!$_[0]->isa('Bio::EnsEMBL::Variation::StructuralVariation') &&
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169 !$_[0]->isa('Bio::EnsEMBL::Variation::SupportingStructuralVariation')
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170 )) {
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171 throw("Bio::EnsEMBL::Variation::StructuralVariation or Bio::EnsEMBL::Variation::SupportingStructuralVariation argument expected");
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172 }
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173 $self->{'_structural_variation_id'} = shift;
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174 }
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175 elsif(!defined($self->{'structural_variation'}) && $self->{'adaptor'} &&
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176 defined($self->{'_structural_variation_id'})) {
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177 # lazy-load from database on demand
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178 my $sva = $self->{'adaptor'}->db()->get_StructuralVariationAdaptor();
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179 $self->{'structural_variation'} = $sva->fetch_by_dbID($self->{'_structural_variation_id'});
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180 if (!defined($self->{'structural_variation'})) {
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181 $sva = $self->{'adaptor'}->db()->get_SupportingStructuralVariationAdaptor();
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182 $self->{'structural_variation'} = $sva->fetch_by_dbID($self->{'_structural_variation_id'});
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183 }
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184 }
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185
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186 return $self->{'structural_variation'};
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187 }
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188
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189
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190 =head2 study
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191
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192 Arg [1] : Bio::EnsEMBL::Variation::Study (optional)
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193 Example : $study = $sv->study()
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194 Description: Getter/Setter for the study object
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195 Returntype : Bio::EnsEMBL::Variation::Study
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196 Exceptions : none
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197 Caller : general
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198 Status : At Risk
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199
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200 =cut
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201
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202 sub study {
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203 my $self = shift;
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204 return $self->{'study'} = shift if(@_);
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205 return $self->{'study'};
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206 }
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207
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208
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209 =head2 study_type
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210
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211 Arg [1] : string study_type (optional)
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212 The new value to set the study_type attribute to
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213 Example : $study_type = $obj->study_type()
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214 Description: Getter/Setter for the study_type attribute.
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215 Returntype : string
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216 Exceptions : none
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217 Caller : general
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218 Status : At Risk
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219
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220 =cut
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221
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222 sub study_type{
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223 my $self = shift;
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224 return $self->{'study'}->type = shift if(@_);
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225 return $self->{'study'}->type;
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226 }
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227
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228
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229 =head2 study_name
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230
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231 Arg [1] : string $study_name (optional)
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232 The new value to set the study_name attribute to
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233 Example : $study = $sva->study_name()
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234 Description: Getter/Setter for the study_name attribute
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235 Returntype : string
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236 Exceptions : none
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237 Caller : general
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238 Status : At Risk
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239
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240 =cut
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241
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242 sub study_name{
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243 my $self = shift;
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244 return $self->{'study'}->name = shift if(@_);
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245 return $self->{'study'}->name;
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246 }
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247
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248
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249 =head2 study_description
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250
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251 Arg [1] : string $study_description (optional)
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252 The new value to set the study_description attribute to
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253 Example : $study_description = $obj->study_description()
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254 Description: Getter/Setter for the study_description attribute
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255 Returntype : string
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256 Exceptions : none
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257 Caller : general
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258 Status : At Risk
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259
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260 =cut
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261
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262 sub study_description{
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263 my $self = shift;
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264 return $self->{'study'}->description = shift if(@_);
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265 return $self->{'study'}->description;
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266 }
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267
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268
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269 =head2 external_reference
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270
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271 Arg [1] : string $newval (optional)
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272 The new value to set the external reference attribute to
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273 Example : $external_reference = $obj->external_reference()
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274 Description: Getter/Setter for the external reference attribute. This is the
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275 pubmed/id or project name associated with this study.
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276 Returntype : string
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277 Exceptions : none
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278 Caller : general
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279 Status : At Risk
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280
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281 =cut
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282
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283 sub external_reference{
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284 my $self = shift;
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285 return $self->{'study'}->external_reference = shift if(@_);
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286 return $self->{'study'}->external_reference;
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287 }
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288
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289
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290 =head2 study_url
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291
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292 Arg [1] : string $newval (optional)
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293 The new value to set the study_url attribute to
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294 Example : $url = $obj->study_url()
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295 Description: Getter/Setter for the study_url attribute. This is the link to the website where the data are stored.
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296 Returntype : string
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297 Exceptions : none
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298 Caller : general
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299 Status : At Risk
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300
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301 =cut
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302
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303 sub study_url{
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304 my $self = shift;
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305 return $self->{'study'}->url = shift if(@_);
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306 return $self->{'study'}->url;
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307 }
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308
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309
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310 =head2 sample_name
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311
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312 Arg [1] : string sample_name (optional)
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313 The new value to set the sample attribute to
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314 Example : $sample_name = $obj->sample_name()
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315 Description: Getter/Setter for the sample attribute.
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316 Returntype : string
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317 Exceptions : none
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318 Caller : general
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319 Status : At Risk
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320
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321 =cut
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322
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323 sub sample_name {
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324 my $self = shift;
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325 return $self->{'sample_name'} = shift if(@_);
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326 return $self->{'sample_name'};
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327 }
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328
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329
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330 =head2 strain_name
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331
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332 Arg [1] : string strain_name (optional)
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333 The new value to set the strain attribute to
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334 Example : $strain_name = $obj->strain_name()
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335 Description: Getter/Setter for the strain attribute.
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336 Returntype : string
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337 Exceptions : none
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338 Caller : general
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339 Status : At Risk
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340
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341 =cut
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342
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343 sub strain_name {
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344 my $self = shift;
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345 return $self->{'strain_name'} = shift if(@_);
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346 return $self->{'strain_name'};
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347 }
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348
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349
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350 =head2 phenotype_description
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351
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352 Arg [1] : string phenotype_description (optional)
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353 The new value to set the phenotype_description attribute to
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354 Example : $phenotype_description = $obj->phenotype_description()
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355 Description: Getter/Setter for the phenotype_description attribute.
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356 Returntype : string
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357 Exceptions : none
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358 Caller : general
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359 Status : At Risk
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360
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361 =cut
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362
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363 sub phenotype_description{
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364 my $self = shift;
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365 return $self->{'phenotype_description'} = shift if(@_);
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366 return $self->{'phenotype_description'};
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367 }
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368
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369
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370 =head2 clinical_significance
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371
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372 Arg [1] : string clinical_significance (optional)
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373 The new value to set the clinical significance attribute to
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374 Example : $clinical_significance = $obj->clinical_significance()
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375 Description: Getter/Setter for the clinical significance attribute.
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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 Status : At Risk
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380
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381 =cut
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382
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383 sub clinical_significance {
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384 my $self = shift;
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385 return $self->{'clinical_significance'} = shift if(@_);
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386 return $self->{'clinical_significance'};
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387 }
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388
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389 1;
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