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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::IdMapping::TinyGene - lightweight gene object
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24
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25 =head1 SYNOPSIS
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26
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27 # fetch a gene from the db and create a lightweight gene object from it
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28 my $gene = $gene_adaptor->fetch_by_stable_id('ENSG000345437');
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29 my $lightweight_gene = Bio::EnsEMBL::IdMapping::TinyGene->new_fast( [
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30 $gene->dbID, $gene->stable_id,
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31 $gene->version, $gene->created_date,
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32 $gene->modified_date, $gene->start,
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33 $gene->end, $gene->strand,
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34 $gene->slice->seq_region_name, $gene->biotype,
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35 $gene->status, $gene->analysis->logic_name,
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36 ( $gene->is_known ? 1 : 0 ),
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37 ] );
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38
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39 =head1 DESCRIPTION
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40
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41 This is a lightweight gene object for the stable Id mapping. See the
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42 documentation in TinyFeature for general considerations about its
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43 design.
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44
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45 =head1 METHODS
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46
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47 start
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48 end
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49 strand
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50 seq_region_name
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51 biotype
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52 status
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53 logic_name
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54 is_known
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55 add_Transcript
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56 get_all_Transcripts
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57 length
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58
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59 =cut
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60
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61 package Bio::EnsEMBL::IdMapping::TinyGene;
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62
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63 # internal data structure (array indices):
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64 #
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65 # 0-4 see TinyFeature
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66 # 5 start
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67 # 6 end
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68 # 7 strand
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69 # 8 seq_region_name
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70 # 9 biotype
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71 # 10 status
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72 # 11 logic_name
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73 # 12 is_known
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74 # 13 [transcripts]
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75
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76
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77 use strict;
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78 use warnings;
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79 no warnings 'uninitialized';
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80
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81 use Bio::EnsEMBL::IdMapping::TinyFeature;
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82 our @ISA = qw(Bio::EnsEMBL::IdMapping::TinyFeature);
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83
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84 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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85
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86
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87 =head2 start
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88
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89 Arg[1] : (optional) Int - the gene's start coordinate
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90 Description : Getter/setter for the gene's start coordinate.
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91 Return type : Int
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92 Exceptions : none
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93 Caller : general
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94 Status : At Risk
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95 : under development
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96
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97 =cut
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98
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99 sub start {
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100 my $self = shift;
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101 $self->[5] = shift if (@_);
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102 return $self->[5];
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103 }
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104
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105
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106 =head2 end
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107
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108 Arg[1] : (optional) Int - the gene's end coordinate
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109 Description : Getter/setter for the gene's end coordinate.
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110 Return type : Int
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111 Exceptions : none
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112 Caller : general
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113 Status : At Risk
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114 : under development
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115
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116 =cut
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117
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118 sub end {
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119 my $self = shift;
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120 $self->[6] = shift if (@_);
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121 return $self->[6];
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122 }
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123
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124
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125 =head2 strand
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126
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127 Arg[1] : (optional) Int - the gene's strand
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128 Description : Getter/setter for the gene's strand.
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129 Return type : Int
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130 Exceptions : none
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131 Caller : general
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132 Status : At Risk
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133 : under development
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134
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135 =cut
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136
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137 sub strand {
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138 my $self = shift;
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139 $self->[7] = shift if (@_);
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140 return $self->[7];
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141 }
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142
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143
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144 =head2 seq_region_name
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145
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146 Arg[1] : (optional) String - seq_region name
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147 Description : Getter/setter for the seq_region name of the slice the gene is
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148 on.
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149 Return type : String
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150 Exceptions : none
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151 Caller : general
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152 Status : At Risk
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153 : under development
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154
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155 =cut
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156
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157 sub seq_region_name {
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158 my $self = shift;
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159 $self->[8] = shift if (@_);
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160 return $self->[8];
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161 }
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162
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163
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164 =head2 biotype
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165
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166 Arg[1] : (optional) String - the gene's biotype
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167 Description : Getter/setter for the gene's biotype.
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168 Return type : String
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169 Exceptions : none
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170 Caller : general
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171 Status : At Risk
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172 : under development
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173
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174 =cut
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175
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176 sub biotype {
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177 my $self = shift;
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178 $self->[9] = shift if (@_);
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179 return $self->[9];
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180 }
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181
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182
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183 =head2 strand
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184
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185 Arg[1] : (optional) String - the gene's status
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186 Description : Getter/setter for the gene's status.
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187 Return type : String
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188 Exceptions : none
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189 Caller : general
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190 Status : At Risk
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191 : under development
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192
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193 =cut
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194
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195 sub status {
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196 my $self = shift;
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197 $self->[10] = shift if (@_);
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198 return $self->[10];
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199 }
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200
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201
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202 =head2 logic_name
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203
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204 Arg[1] : (optional) String - the gene's analysis' logic_name
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205 Description : Getter/setter for the gene's analysis' logic_name.
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206 Return type : String
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207 Exceptions : none
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208 Caller : general
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209 Status : At Risk
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210 : under development
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211
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212 =cut
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213
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214 sub logic_name {
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215 my $self = shift;
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216 $self->[11] = shift if (@_);
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217 return $self->[11];
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218 }
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219
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220
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221 =head2 is_known
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222
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223 Arg[1] : (optional) Boolean - the gene's "known" status
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224 Description : Getter/setter for the gene's "known" status.
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225 Return type : Boolean
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226 Exceptions : none
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227 Caller : general
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228 Status : At Risk
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229 : under development
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230
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231 =cut
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232
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233 sub is_known {
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234 my $self = shift;
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235 $self->[12] = shift if (@_);
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236 return $self->[12];
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237 }
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238
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239
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240 =head2 add_Transcript
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241
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242 Arg[1] : Bio::EnsEMBL::IdMapping::TinyTranscript $tr - the transcript to
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243 add
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244 Example : $tiny_gene->add_Transcript($tiny_transcript);
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245 Description : Adds a transcript to a gene.
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246 Return type : none
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247 Exceptions : thrown on wrong or missing argument
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248 Caller : general
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249 Status : At Risk
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250 : under development
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251
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252 =cut
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253
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254 sub add_Transcript {
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255 my $self = shift;
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256 my $tr = shift;
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257
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258 unless ($tr && $tr->isa('Bio::EnsEMBL::IdMapping::TinyTranscript')) {
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259 throw('Need a Bio::EnsEMBL::IdMapping::TinyTranscript.');
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260 }
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261
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262 push @{ $self->[13] }, $tr;
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263 }
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264
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265
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266 =head2 get_all_Transcripts
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267
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268 Example : foreach my $tr (@{ $tiny_gene->get_all_Transcripts }) {
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269 # do something with transcript
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270 }
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271 Description : Returns all transcripts attached to that gene.
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272 Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyTranscript objects
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273 Exceptions : none
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274 Caller : general
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275 Status : At Risk
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276 : under development
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277
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278 =cut
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279
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280 sub get_all_Transcripts {
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281 return $_[0]->[13] || [];
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282 }
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283
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284
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285 =head2 length
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286
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287 Description : Returns the gene length (distance between start and end).
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288 Return type : Int
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289 Exceptions : none
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290 Caller : general
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291 Status : At Risk
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292 : under development
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293
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294 =cut
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295
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296 sub length {
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297 my $self = shift;
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298 return ($self->end - $self->start + 1);
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299 }
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300
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301
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302 1;
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303
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