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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::DBSQL::MetaContainer - Encapsulates all access to core
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24 database meta information
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25
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26 =head1 SYNOPSIS
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27
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28 my $meta_container =
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29 $registry->get_adaptor( 'Human', 'Core', 'MetaContainer' );
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30
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31 my @mapping_info =
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32 @{ $meta_container->list_value_by_key('assembly.mapping') };
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33
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34 my $scientific_name = $meta_container->get_scientific_name();
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35
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36 =head1 DESCRIPTION
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37
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38 An object that encapsulates specific access to core db meta data
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39
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40 =head1 METHODS
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41
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42 =cut
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43
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44 package Bio::EnsEMBL::DBSQL::MetaContainer;
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45
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46 use strict;
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47 use warnings;
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48
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49 use Bio::EnsEMBL::Utils::Exception qw/deprecate/;
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50 use Bio::Species;
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51
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52
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53 use base qw/Bio::EnsEMBL::DBSQL::BaseMetaContainer/;
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54
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55 # add well known meta info get-functions below
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56
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57 =head2 get_production_name
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58
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59 Args : none
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60 Example : $species = $meta_container->get_production_name();
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61 Description : Obtains the name of the species in a form usable as, for
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62 example, a table name, file name etc.
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63 Returntype : string
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64 Exceptions : none
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65 Status : Stable
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66
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67 =cut
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68
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69 sub get_production_name {
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70 my ($self) = @_;
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71 return $self->single_value_by_key('species.production_name');
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72 }
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73
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74 =head2 get_short_name
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75
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76 Args : none
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77 Example : $species = $meta_container->get_short_name();
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78 Description : Obtains the name of the species in a form usable as, for
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79 example, a short label in a GUI.
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80 Returntype : string
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81 Exceptions : none
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82 Status : Stable
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83
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84 =cut
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85
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86 sub get_short_name {
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87 my ($self) = @_;
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88 return $self->single_value_by_key('species.short_name');
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89 }
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90
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91 =head2 get_common_name
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92
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93 Args : none
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94 Example : $species = $meta_container->get_common_name();
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95 Description : Obtains the common name of the species.
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96 Returntype : string
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97 Exceptions : none
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98 Status : Stable
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99
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100 =cut
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101
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102 sub get_common_name {
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103 my ($self) = @_;
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104 return $self->single_value_by_key('species.common_name');
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105 }
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106
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107 =head2 get_scientific_name
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108
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109 Args : none
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110 Example : $species = $meta_container->get_scientific_name();
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111 Description : Obtains the full scientific name of the species.
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112 Returntype : string
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113 Exceptions : none
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114 Status : Stable
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115
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116 =cut
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117 sub get_scientific_name {
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118 my ($self) = @_;
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119 return $self->single_value_by_key('species.scientific_name');
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120 }
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121
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122 =head2 get_division
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123
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124 Args : none
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125 Example : $div = $meta_container->get_division();
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126 Description : Obtains the Ensembl Genomes division to which the species belongs.
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127 Returntype : string
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128 Exceptions : none
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129 Status : Stable
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130
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131 =cut
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132 sub get_division {
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133 my ($self) = @_;
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134 return $self->single_value_by_key('species.division');
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135 }
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136
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137 =head2 get_Species
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138
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139 Arg [1] : none
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140 Example : $species = $meta_container->get_Species();
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141 Description: Obtains the species from this databases meta table. Call is
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142 deprecated; please use other subroutines in this package
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143 Returntype : Bio::Species
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144 Exceptions : none
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145 Caller : ?
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146 Status : Deprecated
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147
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148 =cut
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149
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150 sub get_Species {
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151 my ($self) = @_;
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152
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153 deprecate('Call is deprecated. Use $self->get_common_name() / $self->get_classification() / $self->get_scientific_name() instead');
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154
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155 my $common_name = $self->get_common_name();
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156 my $classification =
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157 $self->list_value_by_key('species.classification');
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158 if ( !@$classification ) {
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159 return undef;
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160 }
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161
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162 #Re-create the old classification data structure by adding the scientific
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163 #name back onto the classification but with species before genus e.g.
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164 # sapiens -> Homo -> Hominade
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165 my $scientific_name = $self->get_scientific_name();
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166 my ($genus, @sp) = split(/ /, $scientific_name);
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167 unshift(@{$classification}, join(q{ }, @sp), $genus);
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168
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169 my $species = Bio::Species->new();
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170 $species->common_name($common_name);
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171
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172 $species->classification($classification, 1); #always force it
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173
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174 return $species;
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175 }
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176
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177
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178 =head2 get_taxonomy_id
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179
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180 Arg [1] : none
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181 Example : $tax_id = $meta_container->get_taxonomy_id();
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182 Description: Retrieves the taxonomy id from the database meta table
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183 Returntype : string
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184 Exceptions : none
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185 Caller : ?
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186 Status : Stable
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187
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188 =cut
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189
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190 sub get_taxonomy_id {
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191 my ($self) = @_;
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192 return $self->single_value_by_key('species.taxonomy_id', 1);
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193 }
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194
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195
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196
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197 =head2 get_default_assembly
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198
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199 Description: DEPRECATED. Use the version of the coordinate system you are
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200 interested in instead.
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201
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202 Example: #use this instead
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203 my ($highest_cs) = @{$db->get_CoordSystemAdaptor->fetch_all()};
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204 my $assembly = $highest_cs->version();
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205
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206 =cut
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207
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208 sub get_default_assembly {
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209 my $self = shift;
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210
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211 deprecate("Use version of coordinate system you are interested in instead.\n".
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212 "Example:\n".
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213 ' ($cs) = @{$coord_system_adaptor->fetch_all()};'."\n" .
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214 ' $assembly = $cs->version();');
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215
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216 my ($cs) = @{$self->db->get_CoordSystemAdaptor->fetch_all()};
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217
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218 return $cs->version();
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219 }
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220
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221
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222 #
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223 # TBD This method should be removed/deprecated
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224 #
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225 sub get_max_assembly_contig {
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226 my $self = shift;
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227 deprecate('This method should either be fixed or removed');
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228 return $self->single_value_by_key('assembly.maxcontig');
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229 }
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230
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231 =head2 get_genebuild
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232
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233 Arg [1] : none
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234 Example : $tax_id = $meta_container->get_genebuild();
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235 Description: Retrieves the genebuild from the database meta table
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236 Returntype : string
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237 Exceptions : none
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238 Caller : ?
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239 Status : Stable
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240
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241 =cut
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242
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243 sub get_genebuild {
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244 my ($self) = @_;
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245 return $self->single_value_by_key('genebuild.start_date', 1);
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246 }
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247
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248 =head2 get_genebuild
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249
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250 Example : $classification = $meta_container->get_classification();
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251 Description: Retrieves the classification held in the backing database minus
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252 any species specific levels. This means that the first element
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253 in the array will be subfamily/family level ascending to
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254 superkingdom
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255 Returntype : ArrayRef[String]
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256 Exceptions : none
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257 Caller : ?
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258 Status : Stable
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259
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260 =cut
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261
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262 sub get_classification {
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263 my ($self) = @_;
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264 my $classification = $self->list_value_by_key('species.classification');
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265 my $copy = [@{$classification}];
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266 splice(@{$copy}, 0, 1); # remove the Homo sapiens
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267 return $copy;
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268 }
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269
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270
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271 1;
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272
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