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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::VariationAnnotation
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22 #
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23 # Copyright (c) 2004 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::VariationAnnotation - A genotype phenotype annotation for a nucleotide variation.
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30
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31 =head1 SYNOPSIS
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32
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33 # Variation Annotation is associated with a variation object
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34 $va = Bio::EnsEMBL::Variation::VariationAnnotation->new
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35 (_variation_id => 8,
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36 -phenotype_name => 'BD',
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37 -phenotype_description => 'Bipolar Disorder',,
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38 -associated_gene => 'HHEX',
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39 -associated_variant_risk_allele => 'rs13266634-C',
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40 -variation_names => 'rs13266634',
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41 -risk_allele_freq_in_controls => '0.3',
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42 -p_value => '6.00E-08',
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43 -variation => $v);
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44
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45 ...
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46
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47 print $va->phenotype_name(),'-',$va->phenotype_description,"\n";
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48 print "From source ",$va->source_name,'-',$va->study_name,"\n";
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49 print " With study_type ", $va->study_type(),"\n";
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50
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51 ...
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52 # Get the Variation object which this annotation represents
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53 # If not already retrieved from the DB, this will be
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54 # transparently lazy-loaded
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55 my $v = $va->variation();
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56
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57 =head1 DESCRIPTION
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58
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59 This is a class representing the genotype-phenotype annotation of a variation
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60 from the ensembl-variation database. The actual variation information is
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61 represented by an associated Bio::EnsEMBL::Variation::Variation object.
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62
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63 =head1 METHODS
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64
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65 =cut
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66
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67 use strict;
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68 use warnings;
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69
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70 package Bio::EnsEMBL::Variation::VariationAnnotation;
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71
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72 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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73 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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74 use Bio::EnsEMBL::Variation::Variation;
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75 use Bio::EnsEMBL::Storable;
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76
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77 use vars qw(@ISA);
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78
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79 @ISA = qw(Bio::EnsEMBL::Storable);
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80
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81 =head2 new
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82
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83 Arg [-dbID] :
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84 int - unique internal identifier for variation_annotation
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85 Arg [-ADAPTOR] :
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86 Bio::EnsEMBL::Variation::DBSQL::VariationAnnotationAdaptor
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87 Arg [-PHENOTYPE_NAME] :
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88 string - name of the phenotype
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89 Arg [-PHENOTYPE_DESCRIPTION] :
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90 string - description of the phenotype
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91 Arg [-VARIATION_NAMES] :
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92 string - name of the associated variations
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93 Arg [-VARIATION] :
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94 int - the variation object associated with this annotation.
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95 Arg [_VARIATION_ID] :
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96 int _ the internal id of the variation object associated with this
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97 identifier. This may be provided instead of a variation object so that
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98 the variation may be lazy-loaded from the database on demand.
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99 Arg [-ASSOCIATED_GENE] :
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100 string - the gene names associated with this annotation/variant.
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101 Arg [-ASSOCIATED_VARIANT_RISK_ALLELE] :
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102 string - the variants-risk alleles associated with this annotation.
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103 Arg [-RISK_ALLELE_FREQ_IN_CONTROLS] :
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104 string - the risk allele frequency in controls associated with this annotation.
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105 Arg [-P_VALUE] :
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106 string - the p_value associated with this annotation.
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107 Arg [-STUDY] :
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108 object ref - the study object describing where the annotated variation comes from
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109
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110 Example :
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111 $va = Bio::EnsEMBL::Variation::VariationAnnotation->new
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112 (-phenotype_name => 'BD',
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113 -phenotype_description => 'Bipolar Disorder',
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114 -variation_names => 'rs123',
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115 _variation_id => 10,
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116 -associated_gene => 'HHEX',
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117 -associated_variant_risk_allele => 'rs13266634-C',
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118 -risk_allele_freq_in_controls => '0.3',
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119 -p_value => '6.00E-08',
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120 -variation => $v);
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121
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122 Description: Constructor. Instantiates a new VariationAnnotation object.
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123 Returntype : Bio::EnsEMBL::Variation::VariationAnnotation
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124 Exceptions : none
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125 Caller : general
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126 Status : At Risk
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127
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128 =cut
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129
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130 sub new {
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131 my $caller = shift;
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132 my $class = ref($caller) || $caller;
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133 my $self = $class->SUPER::new(@_);
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134
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135 my ($dbID,$adaptor,$phenotype_id,$phenotype_name,$phenotype_description,$variation_id,$variation_names,
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136 $variation,$associated_gene,$associated_variant_risk_allele,$risk_allele_freq_in_controls,$p_value,
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137 $study) =
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138 rearrange([qw(dbID ADAPTOR _PHENOTYPE_ID PHENOTYPE_NAME PHENOTYPE_DESCRIPTION
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139 VARIATION_ID VARIATION_NAMES VARIATION ASSOCIATED_GENE ASSOCIATED_VARIANT_RISK_ALLELE
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140 RISK_ALLELE_FREQ_IN_CONTROLS P_VALUE STUDY)],@_);
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141
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142 $self->{'dbID'} = $dbID;
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143 $self->{'adaptor'} = $adaptor;
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144 $self->{'_phenotype_id'} = $phenotype_id;
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145 $self->{'phenotype_name'} = $phenotype_name;
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146 $self->{'phenotype_description'} = $phenotype_description;
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147 $self->{'variation'} = $variation;
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148 $self->{'_variation_id'} = $variation_id;
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149 $self->{'variation_names'} = $variation_names;
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150 $self->{'associated_gene'} = $associated_gene;
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151 $self->{'associated_variant_risk_allele'} = $associated_variant_risk_allele;
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152 $self->{'risk_allele_freq_in_controls'} = $risk_allele_freq_in_controls;
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153 $self->{'p_value'} = $p_value;
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154 $self->{'study'} => $study,
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155 return $self;
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156 }
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157
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158
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159
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160 sub new_fast {
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161 my $class = shift;
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162 my $hashref = shift;
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163 return bless $hashref, $class;
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164 }
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165
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166
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167 =head2 phenotype_name
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168
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169 Arg [1] : string phenotype_name (optional)
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170 The new value to set the phenotype_name attribute to
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171 Example : $phenotype_name = $obj->phenotype_name()
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172 Description: Getter/Setter for the phenotype_name attribute.
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173 Returntype : string
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174 Exceptions : none
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175 Caller : general
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176 Status : Stable
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177
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178 =cut
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179
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180 sub phenotype_name{
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181 my $self = shift;
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182 return $self->{'phenotype_name'} = shift if(@_);
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183 return $self->{'phenotype_name'};
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184 }
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185
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186 =head2 phenotype_description
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187
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188 Arg [1] : string phenotype_description (optional)
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189 The new value to set the phenotype_description attribute to
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190 Example : $phenotype_description = $obj->phenotype_description()
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191 Description: Getter/Setter for the phenotype_description attribute.
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192 Returntype : string
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193 Exceptions : none
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194 Caller : general
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195 Status : At Risk
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196
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197 =cut
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198
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199 sub phenotype_description{
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200 my $self = shift;
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201 return $self->{'phenotype_description'} = shift if(@_);
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202 return $self->{'phenotype_description'};
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203 }
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204
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205 =head2 source_name
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206
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207 Arg [1] : string source_name (optional)
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208 The new value to set the source_name attribute to
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209 Example : $source_name = $obj->source_name()
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210 Description: Getter/Setter for the source_name attribute.
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211 Returntype : string
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212 Exceptions : none
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213 Caller : general
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214 Status : At Risk
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215
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216 =cut
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217
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218 sub source_name{
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219 my $self = shift;
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220 return $self->{'study'}->source = shift if(@_);
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221 return $self->{'study'}->source;
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222 }
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223
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224 =head2 study_type
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225
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226 Arg [1] : string study_type (optional)
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227 The new value to set the study_type attribute to
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228 Example : $study_type = $obj->study_type()
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229 Description: Getter/Setter for the study_type attribute.
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230 Returntype : string
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231 Exceptions : none
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232 Caller : general
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233 Status : At Risk
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234
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235 =cut
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236
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237 sub study_type{
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238 my $self = shift;
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239 return $self->{'study'}->type = shift if(@_);
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240 return $self->{'study'}->type;
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241 }
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242
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243
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244 =head2 variation
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245
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246 Arg [1] : (optional) Bio::EnsEMBL::Variation::Variation $variation
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247 Example : $v = $va->variation();
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248 Description: Getter/Setter for the variation associated with this annotation.
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249 If not set, and this VariationAnnotation has an associated adaptor
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250 an attempt will be made to lazy-load the variation from the
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251 database.
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252 Returntype : Bio::EnsEMBL::Variation::Variation
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253 Exceptions : throw on incorrect argument
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254 Caller : general
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255 Status : Stable
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256
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257 =cut
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258
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259 sub variation {
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260 my $self = shift;
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261
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262 if(@_) {
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263 if(!ref($_[0]) || !$_[0]->isa('Bio::EnsEMBL::Variation::Variation')) {
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264 throw("Bio::EnsEMBL::Variation::Variation argument expected");
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265 }
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266 $self->{'variation'} = shift;
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267 }
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268 elsif(!defined($self->{'variation'}) && $self->{'adaptor'} &&
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269 defined($self->{'_variation_id'})) {
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270 # lazy-load from database on demand
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271 my $va = $self->{'adaptor'}->db()->get_VariationAdaptor();
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272 $self->{'variation'} = $va->fetch_by_dbID($self->{'_variation_id'});
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273 }
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274
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275 return $self->{'variation'};
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276 }
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277
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278 =head2 variation_names
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279
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280 Arg [1] : string $newval (optional)
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281 The new value to set the variation_names attribute to
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282 Example : $variation_names = $obj->variation_names()
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283 Description: Getter/Setter for the variation_names attribute. This is the
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284 names of the variation associated with this study.
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285 Returntype : string
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286 Exceptions : none
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287 Caller : general
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288 Status : At Risk
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289
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290 =cut
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291
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292 sub variation_names{
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293 my $self = shift;
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294 return $self->{'variation_names'} = shift if(@_);
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295 return $self->{'variation_names'};
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296 }
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297
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298
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299 =head2 study_name
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300
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301 Arg [1] : string $study_name (optional)
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302 The new value to set the study_name attribute to
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303 Example : $study = $sva->study_name()
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304 Description: Getter/Setter for the study_name attribute
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305 Returntype : string
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306 Exceptions : none
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307 Caller : general
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308 Status : At Risk
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309
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310 =cut
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311
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312 sub study_name{
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313 my $self = shift;
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314 return $self->{'study'}->name = shift if(@_);
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315 return $self->{'study'}->name;
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316 }
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317
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318
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319 =head2 study_description
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320
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321 Arg [1] : string $study_description (optional)
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322 The new value to set the study_description attribute to
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323 Example : $study_description = $obj->study_description()
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324 Description: Getter/Setter for the study_description attribute
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325 Returntype : string
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326 Exceptions : none
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327 Caller : general
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328 Status : At Risk
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329
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330 =cut
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331
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332 sub study_description{
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333 my $self = shift;
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334 return $self->{'study'}->description = shift if(@_);
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335 return $self->{'study'}->description;
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336 }
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337
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338
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339 =head2 external_reference
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340
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341 Arg [1] : string $newval (optional)
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342 The new value to set the external reference attribute to
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343 Example : $external_reference = $obj->external_reference()
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344 Description: Getter/Setter for the external reference attribute. This is the
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345 pubmed/id or project name associated with this study.
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346 Returntype : string
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347 Exceptions : none
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348 Caller : general
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349 Status : At Risk
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350
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351 =cut
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352
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353 sub external_reference{
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354 my $self = shift;
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355 return $self->{'study'}->external_reference = shift if(@_);
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356 return $self->{'study'}->external_reference;
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357 }
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358
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359
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360 =head2 study_url
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361
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362 Arg [1] : string $newval (optional)
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363 The new value to set the study_url attribute to
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364 Example : $url = $obj->study_url()
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365 Description: Getter/Setter for the study_url attribute. This is the link to the website where the data are stored.
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366 Returntype : string
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367 Exceptions : none
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368 Caller : general
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369 Status : At Risk
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370
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371 =cut
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372
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373 sub study_url{
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374 my $self = shift;
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375 return $self->{'study'}->url = shift if(@_);
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376 return $self->{'study'}->url;
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377 }
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378
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379
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380 =head2 associated_studies
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381 Example : $name = $obj->associate_studies()
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382 Description: Getter/Setter for the associated_studies attribute
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383 (e.g. EGA studies can be associated to NHGRI studies).
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384 Returntype : reference to list of Bio::EnsEMBL::Variation::Study
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385 Exceptions : none
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386 Caller : general
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387 Status : At Risk
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388
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389 =cut
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390
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391 sub associated_studies{
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392 my $self = shift;
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393 return $self->{'study'}->associated_studies;
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394 }
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395
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396
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397 =head2 associated_gene
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398
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399 Arg [1] : string $newval (optional)
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400 The new value to set the associated_gene attribute to
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401 Example : $associated_gene = $obj->associated_gene()
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402 Description: Getter/Setter for the associated_gene attribute. This is the
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403 gene names associated with this study.
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404 Returntype : string
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405 Exceptions : none
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406 Caller : general
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407 Status : At Risk
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408
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409 =cut
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410
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411 sub associated_gene{
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412 my $self = shift;
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413 return $self->{'associated_gene'} = shift if(@_);
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414 return $self->{'associated_gene'};
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415 }
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416
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417 =head2 associated_variant_risk_allele
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418
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419 Arg [1] : string $newval (optional)
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420 The new value to set the associated_variant_risk_allele attribute to
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421 Example : $associated_variant_risk_allele = $obj->associated_variant_risk_allele()
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422 Description: Getter/Setter for the associated_variant_risk_allele attribute. This is the
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423 associated_variant_risk_allele associated with this study.
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424 Returntype : string
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425 Exceptions : none
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426 Caller : general
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427 Status : At Risk
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428
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429 =cut
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430
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431 sub associated_variant_risk_allele{
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432 my $self = shift;
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433 return $self->{'associated_variant_risk_allele'} = shift if(@_);
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434 return $self->{'associated_variant_risk_allele'};
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435 }
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436
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437 =head2 risk_allele_freq_in_controls
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438
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439 Arg [1] : string $newval (optional)
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440 The new value to set the risk_allele_freq_in_controls attribute to
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441 Example : $risk_allele_freq_in_controls = $obj->risk_allele_freq_in_controls()
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442 Description: Getter/Setter for the risk_allele_freq_in_controls attribute. This is the
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443 risk_allele_freq_in_controls associated with this study.
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444 Returntype : string
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445 Exceptions : none
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446 Caller : general
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447 Status : At Risk
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448
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449 =cut
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450
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451 sub risk_allele_freq_in_controls{
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452 my $self = shift;
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453 return $self->{'risk_allele_freq_in_controls'} = shift if(@_);
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454 return $self->{'risk_allele_freq_in_controls'};
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455 }
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456
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457 =head2 p_value
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458
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459 Arg [1] : string $newval (optional)
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460 The new value to set the p_value attribute to
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461 Example : $p_value = $obj->p_value()
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462 Description: Getter/Setter for the p_value attribute. This is the
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463 p_value associated with this study.
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464 Returntype : string
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465 Exceptions : none
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466 Caller : general
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467 Status : At Risk
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468
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469 =cut
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470
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471 sub p_value{
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472 my $self = shift;
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473 return $self->{'p_value'} = shift if(@_);
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474 return $self->{'p_value'};
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475 }
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476 1;
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