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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::Allele
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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::Allele - A single allele of 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 $allele = Bio::EnsEMBL::Variation::Allele->new
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34 (-allele => 'A',
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35 -frequency => 0.85,
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36 -population => $population);
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37
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38 $delete = Bio::EnsEMBL::Variation::Allele->new
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39 (-allele => '-',
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40 -frequency => 0.15,
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41 -population => $population);
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42
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43 ...
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44
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45 $astr = $a->allele();
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46 $pop = $a->population();
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47 $freq = $a->frequency();
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48
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49 print $a->allele();
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50 if($a->populaton) {
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51 print " found in population ", $allele->population->name();
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52 }
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53 if(defined($a->frequency())) {
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54 print " with frequency ", $a->frequency();
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55 }
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56 print "\n";
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57
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58
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59
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60 =head1 DESCRIPTION
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61
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62 This is a class representing a single allele of a variation. In addition to
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63 the nucleotide(s) (or absence of) that representing the allele frequency
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64 and population information may be present.
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65
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66 =head1 METHODS
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67
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68 =cut
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69
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70 use strict;
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71 use warnings;
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72
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73 package Bio::EnsEMBL::Variation::Allele;
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74
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75 use Bio::EnsEMBL::Storable;
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76 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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77 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
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78 use Bio::EnsEMBL::Utils::Scalar qw(assert_ref check_ref);
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79 use Scalar::Util qw(weaken);
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80 use Bio::EnsEMBL::Variation::Failable;
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81
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82 our @ISA = ('Bio::EnsEMBL::Storable', 'Bio::EnsEMBL::Variation::Failable');
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83
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84
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85 =head2 new
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86
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87 Arg [-dbID]: int - unique internal identifier for the Allele
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88 Arg [-ADAPTOR]: Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor
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89 Arg [-ALLELE]: string - the nucleotide string representing the allele
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90 Arg [-FREQUENCY]: float - the frequency of the allele
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91 Arg [-POPULATION]: Bio::EnsEMBL::Variation::Population - the population
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92 in which the allele was recorded
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93 Example : $allele = Bio::EnsEMBL::Variation::Allele->new
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94 (-allele => 'A',
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95 -frequency => 0.85,
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96 -population => $pop);
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97
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98 Description: Constructor. Instantiates a new Allele object.
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99 Returntype : Bio::EnsEMBL::Variation::Allele
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100 Exceptions : none
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101 Caller : general
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102 Status : At Risk
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103
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104 =cut
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105
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106
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107 sub new {
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108 my $caller = shift;
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109 my $class = ref($caller) || $caller;
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110
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111 my ($dbID, $adaptor, $allele, $freq, $count, $pop, $ss_id, $variation_id, $population_id) =
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112 rearrange(['dbID', 'ADAPTOR', 'ALLELE', 'FREQUENCY', 'COUNT', 'POPULATION', 'SUBSNP', 'VARIATION_ID', 'POPULATION_ID'], @_);
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113
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114 # set subsnp_id to undefined if it's 0 in the DB
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115 #$ss_id = undef if (defined $ss_id && $ss_id == 0);
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116
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117 # add ss to the subsnp_id
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118 $ss_id = 'ss'.$ss_id if defined $ss_id && $ss_id !~ /^ss/;
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119
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120 # Check that we at least get a BaseAdaptor
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121 assert_ref($adaptor,'Bio::EnsEMBL::Variation::DBSQL::BaseAdaptor');
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122 # If the adaptor is not an AlleleAdaptor, try to get it via the passed adaptor
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123 unless (check_ref($adaptor,'Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor')) {
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124 $adaptor = $adaptor->db->get_AlleleAdaptor();
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125 # Verify that we could get the AlleleAdaptor
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126 assert_ref($adaptor,'Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor');
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127 }
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128
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129 my $self = bless {}, $class;
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130
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131 $self->dbID($dbID);
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132 $self->adaptor($adaptor);
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133 $self->allele($allele);
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134 $self->frequency($freq);
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135 $self->count($count);
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136 $self->subsnp($ss_id);
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137 $self->{'_variation_id'} = $variation_id;
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138 $self->{'_population_id'} = $population_id;
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139 $self->population($pop) if (defined($pop));
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140
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141 return $self;
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142 }
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143
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144 sub new_fast {
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145 my $class = shift;
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146 my $hashref = shift;
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147 return bless $hashref, $class;
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148 }
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149
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150
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151 # An internal method for getting a unique hash key identifier, used by the Variation module
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152 sub _hash_key {
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153 my $self = shift;
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154
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155 # By default, return the dbID
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156 my $dbID = $self->dbID();
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157 return $dbID if (defined($dbID));
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158
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159 # If no dbID is specified, e.g. if we are creating a 'custom' object, return a fake dbID. This is necessary since e.g. Variation stores
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160 # its alleles in a hash with dbID as key. To create fake dbIDs, use the string representing the memory address.
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161 ($dbID) = sprintf('%s',$self) =~ m/\(([0-9a-fx]+)\)/i;
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162 return $dbID;
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163 }
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164
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165 =head2 allele
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166
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167 Arg [1] : string $newval (optional)
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168 The new value to set the allele attribute to
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169 Example : print $a->allele();
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170 $a1->allele('A');
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171 $a2->allele('-');
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172 Description: Getter/Setter for the allele attribute. The allele is a string
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173 of nucleotide sequence, or a '-' representing the absence of
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174 sequence (deletion).
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175 Returntype : string
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176 Exceptions : none
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177 Caller : general
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178 Status : At Risk
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179
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180 =cut
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181
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182 sub allele{
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183 my $self = shift;
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184 return $self->{'allele'} = shift if(@_);
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185 return $self->{'allele'};
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186 }
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187
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188
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189
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190
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191 =head2 frequency
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192
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193 Arg [1] : float $newval (optional)
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194 The new value to set the frequency attribute to
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195 Example : $frequency = $a->frequency();
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196 Description: Getter/Setter for the frequency attribute. The frequency is
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197 the frequency of the occurance of the allele. If the population
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198 attribute it is the frequency of the allele within that
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199 population.
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200 Returntype : float
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201 Exceptions : none
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202 Caller : general
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203 Status : At Risk
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204
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205 =cut
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206
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207 sub frequency{
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208 my $self = shift;
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209 return $self->{'frequency'} = shift if(@_);
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210 return $self->{'frequency'};
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211 }
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212
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213 =head2 count
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214
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215 Arg [1] : int $count (optional)
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216 The new value to set the count attribute to
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217 Example : $frequency = $allele->count()
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218 Description: Getter/Setter for the observed count of this allele
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219 within its associated population.
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220 Returntype : string
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221 Exceptions : none
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222 Caller : general
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223 Status : At Risk
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224
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225 =cut
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226
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227 sub count{
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228 my $self = shift;
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229 return $self->{'count'} = shift if(@_);
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230 return $self->{'count'};
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231 }
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232
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233
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234
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235 =head2 population
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236
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237 Arg [1] : Bio::EnsEMBL::Variation::Population $newval (optional)
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238 The new value to set the population attribute to
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239 Example : $population = $a->population();
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240 Description: Getter/Setter for the population attribute
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241 Returntype : Bio::EnsEMBL::Variation::Population
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242 Exceptions : throw on incorrect argument
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243 Caller : general
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244 Status : At Risk
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245
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246 =cut
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247
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248 sub population{
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249 my $self = shift;
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250
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251 if(@_) {
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252 assert_ref($_[0],'Bio::EnsEMBL::Variation::Population');
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253 $self->{'population'} = shift;
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254 $self->{'_population_id'} = $self->{'population'}->dbID();
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255 }
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256
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257 # Population can be lazy-loaded, so get it from the database if we have a sample_id but no cached object
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258 if (!defined($self->{'population'}) && defined($self->{'_population_id'})) {
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259
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260 # Check that an adaptor is attached
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261 assert_ref($self->adaptor(),'Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor');
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262
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263 # Get a population object
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264 my $population = $self->adaptor->db->get_PopulationAdaptor()->fetch_by_dbID($self->{'_population_id'});
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265
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266 # Set the population
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267 $self->{'population'} = $population;
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268 }
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269
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270 return $self->{'population'};
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271 }
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272
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273
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274 =head2 subsnp
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275
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276 Arg [1] : string $newval (optional)
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277 The new value to set the subsnp attribute to
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278 Example : print $a->subsnp();
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279 Description: Getter/Setter for the subsnp attribute.
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280 Returntype : string
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281 Exceptions : none
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282 Caller : general
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283 Status : At Risk
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284
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285 =cut
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286
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287 sub subsnp{
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288 my $self = shift;
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289 if(@_) {
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290 $self->{'subsnp'} = shift;
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291 }
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292
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293 my $ssid = $self->{'subsnp'};
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294 if(defined($ssid)) {
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295 $ssid = 'ss'.$ssid unless $ssid =~ /^ss/;
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296 }
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297
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298 return $ssid;
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299 }
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300
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301
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302 =head2 variation
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303
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304 Arg [1] : Bio::EnsEMBL::Variation::Variation $newval (optional)
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305 The new value to set the variation attribute to
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306 Example : print $a->variation->name();
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307 Description: Getter/Setter for the variation attribute.
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308 Returntype : Bio::EnsEMBL::Variation::Variation
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309 Exceptions : throw on incorrect argument
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310 Caller : general
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311
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312 =cut
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313
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314 sub variation {
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315 my $self = shift;
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316 my $variation = shift;
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317
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318 # Set the dbID of the variation object on this allele
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319 if(defined($variation)) {
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320 assert_ref($variation,'Bio::EnsEMBL::Variation::Variation');
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321 $self->{'_variation_id'} = $variation->dbID();
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322 return $variation;
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323 }
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324
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325 # Load the variation from the database if we have a variation_id
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326 if (defined($self->{'_variation_id'})) {
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327
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328 # Check that an adaptor is attached
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329 assert_ref($self->adaptor(),'Bio::EnsEMBL::Variation::DBSQL::BaseAdaptor');
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330
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331 # Get a variation object
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332 $variation = $self->adaptor->db->get_VariationAdaptor()->fetch_by_dbID($self->{'_variation_id'});
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333
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334 $self->{variation} = $variation;
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335 }
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336
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337 # Return the variation object
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338 return $self->{variation};
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339 }
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340
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341
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342 =head2 subsnp_handle
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343
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344 Arg [1] : string $newval (optional)
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345 The new value to set the subsnp_handle attribute to
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346 Example : print $a->subsnp_handle();
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347 Description: Getter/Setter for the subsnp_handle attribute.
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348 Returntype : string
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349 Exceptions : none
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350 Caller : general
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351 Status : At Risk
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352
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353 =cut
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354
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355 sub subsnp_handle{
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356 my $self = shift;
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357 my $handle = shift;
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358
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359 # if changing handle
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360 if(defined($handle)) {
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361 $self->{'subsnp_handle'} = $handle;
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362 }
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363 elsif (!defined($self->{'subsnp_handle'})) {
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364
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365 # Check that this allele has an adaptor attached
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366 assert_ref($self->adaptor(),'Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor');
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367
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368 $self->{'subsnp_handle'} = $self->adaptor->get_subsnp_handle($self);
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369 }
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370
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371 return $self->{'subsnp_handle'};
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372 }
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373
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374 sub _weaken {
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375 my $self = shift;
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376
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377 # If the variation is not defined, do nothing
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378 return unless (defined($self->variation()));
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379
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380 # Weaken the link to the variation
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381 weaken($self->{'variation'});
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382 }
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383
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384 1;
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