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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 =head1 NAME
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22
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23 Bio::EnsEMBL::Map::Qtl
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24
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25 =head1 SYNOPSIS
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26
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27 =head1 DESCRIPTION
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28
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29 Represents a Qtl in the EnsEMBL database. A quantitative trait locus is
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30 defined by three markers, two flanking and one peak (optional) marker.
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31 Its a region (or more often a group of regions) which is likely to
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32 affect the phenotype (trait) described in this Qtl.
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33
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34 =head1 METHODS
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35
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36 =cut
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37
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38 package Bio::EnsEMBL::Map::Qtl;
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39
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40 use strict;
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41 use vars qw(@ISA);
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42
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43 use Bio::EnsEMBL::Storable;
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44 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
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45
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46 @ISA = qw(Bio::EnsEMBL::Storable);
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47
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48
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49
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50 =head2 new
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51
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52 Arg [1] : int $dbID
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53 Arg [2] : Bio::EnsEMBL::Map::DBSQL::QtlAdaptor $adaptor
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54 Arg [3] : Bio::EnsEMBL::Map::Marker $flank_marker_1
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55 Arg [4] : Bio::EnsEMBL::Map::Marker $peak_marker
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56 Arg [5] : Bio::EnsEMBL::Map::Marker $flank_marker_2
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57 Arg [6] : string $trait
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58 Arg [7] : float $lod_score
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59 Arg [8] : hashref $synonyms
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60 A hashref with source keys and identifier values
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61 Example : none
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62 Description: Creates a new Qtl object. Usually done by Adaptor
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63 Returntype : Bio::EnsEMBL::Map::Qtl
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64 Exceptions : none
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65 Caller : general, DBSQL::QtlAdaptor, DBSQL::QtlFeatureAdaptor
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66 Status : stable
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67
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68 =cut
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69
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70 sub new {
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71 my ( $class, $dbID, $adaptor, $flank_marker_1, $peak_marker,
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72 $flank_marker_2, $trait, $lod_score,
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73 $synonyms ) = @_;
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74
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75 $class = ref( $class ) ||$class;
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76 my $self = bless( {
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77 'dbID' => $dbID,
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78 'flank_marker_1' => $flank_marker_1,
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79 'flank_marker_2' => $flank_marker_2,
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80 'peak_marker' => $peak_marker,
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81 'trait' => $trait,
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82 'lod_score' => $lod_score,
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83 'synonyms' => $synonyms
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84 }, $class );
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85 $self->adaptor($adaptor);
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86 return $self;
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87 }
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88
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89
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90 =head2 add_synonym
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91
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92 Arg [1] : string $source
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93 The source of the synonym
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94 Arg [2] : string $identifier
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95 The identifier from this source
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96 Example : $qtl->add_synonym('rat genome database', '65516');
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97 Description: Adds a synonym to this qtl
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98 Returntype : none
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99 Exceptions : thrown if arguments are not provided
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100 Caller : general
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101 Status : stable
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102
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103 =cut
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104
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105 sub add_synonym {
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106 my $self = shift;
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107 my $source = shift;
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108 my $identifier = shift;
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109
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110 unless($source && $identifier) {
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111 throw('Source and identifier arguments are required');
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112 }
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113
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114 $self->{'synonyms'}->{$source} = $identifier;
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115 }
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116
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117
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118 =head2 get_synonyms
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119
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120 Arg [1] : none
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121 Example :
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122 foreach my $source ($keys %{$qtl->get_synonyms}) {
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123 print $source . ':'. $qtl->get_synonyms->{$source};
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124 }
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125 Description: Returns a hashref of synonyms keyed on their source name
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126 Returntype : hashref of synonyms keyed on their source name
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127 Exceptions : none
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128 Caller : general
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129 Status : stable
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130
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131 =cut
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132
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133 sub get_synonyms {
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134 my $self = shift;
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135
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136 return $self->{'synonyms'} || {};
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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 =head2 trait
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142
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143 Arg [1] : string $trait
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144 Phenotype of this Qtl
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145 Example : none
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146 Description: Getter/Setter for the trait attribute
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147 Returntype : string
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148 Exceptions : none
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149 Caller : general
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150 Status : stable
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151
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152 =cut
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153
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154 sub trait {
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155 my $self = shift;
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156
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157 if(@_) {
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158 $self->{'trait'} = shift;
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159 }
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160
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161 return $self->{'trait'};
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162 }
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163
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164
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165 =head2 lod_score
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166
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167 Arg [1] : float $lod_score
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168 A score for the Qtl
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169 Example : none
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170 Description: Getter/Setter for attribute lod_score
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171 Returntype : float
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172 Exceptions : none
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173 Caller : general
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174 Status : stable
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175
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176 =cut
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177
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178 sub lod_score {
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179 my $self = shift;
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180
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181 if(@_) {
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182 $self->{'lod_score'} = shift;
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183 }
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184
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185 return $self->{'lod_score'};
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186 }
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187
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188
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189 =head2 peak_marker
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190
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191 Arg [1] : Bio::EnsEMBL::Map::Marker $peak_marker
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192 an optional Marker which has the peak probablitity
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193 for this traits occurence
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194 Example : none
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195 Description: Getter/Setter for attribute peak_marker
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196 Returntype : Bio::EnsEMBL::Map::Marker
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197 Exceptions : none
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198 Caller : general
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199 Status : stable
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200
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201 =cut
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202
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203 sub peak_marker {
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204 my $self = shift;
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205
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206 if(@_) {
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207 $self->{'peak_marker'} = shift;
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208 }
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209
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210 return $self->{'peak_marker'};
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211 }
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212
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213
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214 =head2 flank_marker_1
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215
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216 Arg [1] : Bio::EnsEMBL::Map::Marker $flank_marker_1
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217 One flanking marker of the interest region, the two flanking
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218 markers define the region
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219 Example : none
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220 Description: Getter/Setter attribute flanking_marker_1
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221 Returntype : Bio::EnsEMBL::Map::Marker
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222 Exceptions : none
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223 Caller : general
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224 Status : stable
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225
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226 =cut
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227
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228 sub flank_marker_1 {
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229 my $self = shift;
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230
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231 if(@_) {
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232 $self->{'flank_marker_1'} = shift;
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233 }
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234
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235 return $self->{'flank_marker_1'};
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236 }
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237
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238
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239
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240 =head2 flank_marker_2
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241
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242 Arg [1] : Bio::EnsEMBL::Map::Marker $flank_marker_2
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243 One flanking marker of the interest region, the two flanking
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244 markers define the region
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245 Example : none
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246 Description: Getter/Setter attribute flanking_marker_2
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247 Returntype : Bio::EnsEMBL::Map::Marker
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248 Exceptions : none
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249 Caller : general
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250 Status : stable
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251
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252 =cut
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253
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254
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255 sub flank_marker_2 {
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256 my $self = shift;
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257
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258 if(@_) {
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259 $self->{'flank_marker_2'} = shift;
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260 }
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261
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262 return $self->{'flank_marker_2'};
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263 }
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264
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265
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266
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267 =head2 get_QtlFeatures
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268
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269 Args : none
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270 Example : none
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271 Description: return the qtl feature which is associated with this
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272 Qtl. It comes in chromosomal slice coordinates. There can
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273 only be one.
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274 Returntype : Bio::EnsEMBL::Map::QtlFeature
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275 Exceptions : only works with adaptored Qtls
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276 Caller : general
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277 Status : stable
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278
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279 =cut
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280
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281 sub get_QtlFeature {
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282 my $self = shift;
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283
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284 my $adaptor = $self->adaptor();
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285 return undef unless $adaptor;
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286 my $result = $adaptor->db()->get_QtlFeatureAdaptor()->
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287 fetch_all_by_Qtl( $self );
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288
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289 if( @$result ) {
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290 return $result->[0];
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291 } else {
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292 return;
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293 }
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294 }
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295
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296
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297
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298
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299
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300 =head2 source_database
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301
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302 This method is deprecated. Use get_synonyms or add_synonym instead.
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303
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304 =cut
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305
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306 sub source_database {
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307 my $self = shift;
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308
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309 deprecate('Use get_synonyms or add_synonym instead');
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310
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311 my $syns = $self->get_synonyms;
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312 my ($source) = keys %$syns;
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313
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314 return $source || '';
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315 }
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316
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317
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318 =head2 source_primary_id
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319
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320 This method is deprecated. Use get_synonyms or add_synonym instead.
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321
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322 =cut
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323
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324 sub source_primary_id {
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325 my $self = shift;
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326
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327 deprecate('Use get_synonyms or add_synonym instead');
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328
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329 my $syns = $self->get_synonyms;
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330 my ($source) = keys %$syns;
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331
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332 if($source) {
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333 return $syns->{$source};
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334 }
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335
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336 return '';
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337 }
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338
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339
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340 1;
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