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2 =head1 LICENSE
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3
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4 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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5 Genome Research Limited. All rights reserved.
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6
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7 This software is distributed under a modified Apache license.
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8 For license details, please see
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9
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10 http://www.ensembl.org/info/about/code_licence.html
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11
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12 =head1 CONTACT
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13
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14 Please email comments or questions to the public Ensembl
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15 developers list at <dev@ensembl.org>.
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16
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17 Questions may also be sent to the Ensembl help desk at
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18 <helpdesk@ensembl.org>.
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19
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20 =cut
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21
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22 =head1 NAME
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23
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24 Bio::EnsEMBL::Operon - Object representing an operon
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25
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26 =head1 SYNOPSIS
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27
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28 my $operon = Bio::EnsEMBL::Operon->new(
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29 -START => 123,
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30 -END => 1045,
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31 -STRAND => 1,
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32 -SLICE => $slice,
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33 -DISPLAY_LABEL => $name
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34 );
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35
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36 # print operon information
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37 print("operon start:end:strand is "
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38 . join( ":", map { $operon->$_ } qw(start end strand) )
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39 . "\n" );
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40
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41 =head1 DESCRIPTION
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42
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43 A representation of an Operon within the Ensembl system.
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44 An operon is a collection of one or more polycistronic transcripts which contain one or more genes.
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45
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46 =head1 METHODS
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47
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48 =cut
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49
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50 package Bio::EnsEMBL::Operon;
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51
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52 use strict;
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53 use warnings;
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54
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55 use Bio::EnsEMBL::Feature;
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56 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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57 use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
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58 use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
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59
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60 use vars qw(@ISA);
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61 @ISA = qw(Bio::EnsEMBL::Feature);
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62
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63 =head2 new
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64
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65 Arg [-START] :
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66 int - start postion of the operon
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67 Arg [-END] :
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68 int - end position of the operon
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69 Arg [-STRAND] :
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70 int - 1,-1 the strand the operon is on
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71 Arg [-SLICE] :
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72 Bio::EnsEMBL::Slice - the slice the operon is on
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73 Arg [-STABLE_ID] :
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74 string - the stable identifier of this operon
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75 Arg [-VERSION] :
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76 int - the version of the stable identifier of this operon
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77 Arg [-DISPLAY_LABEL]:
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78 A name/label for this operon
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79 Arg [-CREATED_DATE]:
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80 string - the date the operon was created
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81 Arg [-MODIFIED_DATE]:
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82 string - the date the operon was last modified
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83
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84 Example : $gene = Bio::EnsEMBL::Operon->new(...);
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85 Description: Creates a new operon object
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86 Returntype : Bio::EnsEMBL::Operon
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87 Exceptions : none
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88 Caller : general
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89 Status : Stable
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90
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91 =cut
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92
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93 sub new {
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94 my $caller = shift;
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95
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96 my $class = ref($caller) || $caller;
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97 my $self = $class->SUPER::new(@_);
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98 my ( $stable_id, $version, $created_date, $modified_date,$display_label) =
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99 rearrange( [ 'STABLE_ID', 'VERSION',
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100 'CREATED_DATE', 'MODIFIED_DATE',
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101 'DISPLAY_LABEL' ],
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102 @_ );
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103
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104 $self->stable_id($stable_id);
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105 $self->version($version);
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106 $self->{'created_date'} = $created_date;
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107 $self->{'modified_date'} = $modified_date;
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108 $self->display_label($display_label);
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109
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110 return $self;
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111 }
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112
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113 =head2 created_date
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114
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115 Arg [1] : (optional) String - created date to set (as a UNIX time int)
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116 Example : $gene->created_date('1141948800');
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117 Description: Getter/setter for attribute created_date
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118 Returntype : String
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119 Exceptions : none
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120 Caller : general
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121 Status : Stable
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122
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123 =cut
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124
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125 sub created_date {
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126 my $self = shift;
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127 $self->{'created_date'} = shift if ( @_ );
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128 return $self->{'created_date'};
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129 }
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130
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131
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132 =head2 modified_date
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133
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134 Arg [1] : (optional) String - modified date to set (as a UNIX time int)
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135 Example : $gene->modified_date('1141948800');
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136 Description: Getter/setter for attribute modified_date
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137 Returntype : String
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138 Exceptions : none
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139 Caller : general
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140 Status : Stable
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141
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142 =cut
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143
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144 sub modified_date {
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145 my $self = shift;
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146 $self->{'modified_date'} = shift if ( @_ );
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147 return $self->{'modified_date'};
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148 }
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149
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150
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151 =head2 display_label
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152
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153 Arg [1] : (optional) String - the name/label to set
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154 Example : $operon->name('accBCD');
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155 Description: Getter/setter for attribute name.
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156 Returntype : String or undef
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157 Exceptions : none
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158 Caller : general
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159 Status : Stable
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160
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161 =cut
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162
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163 sub display_label {
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164 my $self = shift;
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165 $self->{'display_label'} = shift if (@_);
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166 return $self->{'display_label'};
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167 }
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168
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169 =head2 stable_id
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170
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171 Arg [1] : (optional) String - the stable ID to set
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172 Example : $operon->stable_id("accR2");
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173 Description: Getter/setter for stable id for this operon.
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174 Returntype : String
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175 Exceptions : none
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176 Caller : general
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177 Status : Stable
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178
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179 =cut
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180
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181 sub stable_id {
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182 my $self = shift;
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183 $self->{'stable_id'} = shift if (@_);
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184 return $self->{'stable_id'};
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185 }
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186
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187 =head2 version
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188
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189 Arg [1] : (optional) Int - the stable ID version to set
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190 Example : $operon->version(1);
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191 Description: Getter/setter for stable id version for this operon.
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192 Returntype : Int
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193 Exceptions : none
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194 Caller : general
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195 Status : Stable
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196
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197 =cut
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198 sub version {
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199 my $self = shift;
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200 $self->{'version'} = shift if(@_);
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201 return $self->{'version'};
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202 }
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203
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204 =head2 get_all_OperonTranscripts
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205
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206 Example : my $ots = $operon->get_all_OperonTranscripts();
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207 Description: Retrieve all operon transcripts belonging to this operon
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208 Returntype : Arrayref of Bio::EnsEMBL::OperonTranscript
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209 Exceptions : none
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210 Caller : general
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211 Status : Stable
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212
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213 =cut
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214 sub get_all_OperonTranscripts {
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215 my $self = shift;
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216 if ( !exists $self->{'_operon_transcript_array'} ) {
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217 if ( defined $self->adaptor() ) {
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218 my $ta = $self->adaptor()->db()->get_OperonTranscriptAdaptor();
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219 my $transcripts = $ta->fetch_all_by_Operon($self);
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220 $self->{'_operon_transcript_array'} = $transcripts;
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221 }
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222 }
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223 return $self->{'_operon_transcript_array'};
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224 }
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225
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226 =head2 add_OperonTranscript
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227
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228 Arg [1] : Bio::EnsEMBL::OperonTranscript - operon transcript to attach to this operon
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229 Example : $operon->add_OperonTranscript($ot);
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230 Description: Attach a polycistronic operon transcript to this operon
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231 Exceptions : if argument is not Bio::EnsEMBL::OperonTranscript
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232 Caller : general
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233 Status : Stable
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234
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235 =cut
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236 sub add_OperonTranscript {
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237 my ( $self, $trans ) = @_;
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238
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239 assert_ref($trans,"Bio::EnsEMBL::OperonTranscript");
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240
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241 $self->{'_operon_transcript_array'} ||= [];
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242 push( @{ $self->{'_operon_transcript_array'} }, $trans );
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243
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244 #$self->recalculate_coordinates();
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245 return;
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246 }
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247
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248 =head2 add_DBEntry
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249
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250 Arg [1] : Bio::EnsEMBL::DBEntry $dbe
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251 The dbEntry to be added
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252 Example : my $dbe = Bio::EnsEMBL::DBEntery->new(...);
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253 $operon->add_DBEntry($dbe);
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254 Description: Associates a DBEntry with this operon. Note that adding DBEntries
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255 will prevent future lazy-loading of DBEntries for this operon
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256 (see get_all_DBEntries).
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257 Returntype : none
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258 Exceptions : thrown on incorrect argument type
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259 Caller : general
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260 Status : Stable
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261
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262 =cut
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263
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264 sub add_DBEntry {
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265 my $self = shift;
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266 my $dbe = shift;
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267
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268 unless($dbe && ref($dbe) && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
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269 throw('Expected DBEntry argument');
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270 }
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271
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272 $self->{'dbentries'} ||= [];
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273 push @{$self->{'dbentries'}}, $dbe;
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274 }
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275
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276
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277 =head2 get_all_Attributes
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278
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279 Arg [1] : (optional) String $attrib_code
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280 The code of the attribute type to retrieve values for
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281 Example : my ($author) = @{ $operon->get_all_Attributes('author') };
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282 my @operon_attributes = @{ $operon->get_all_Attributes };
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283 Description: Gets a list of Attributes of this operon.
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284 Optionally just get Attributes for given code.
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285 Returntype : Listref of Bio::EnsEMBL::Attribute
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286 Exceptions : warning if gene does not have attached adaptor and attempts lazy
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287 load.
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288 Caller : general
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289 Status : Stable
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290
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291 =cut
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292
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293 sub get_all_Attributes {
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294 my $self = shift;
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295 my $attrib_code = shift;
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296
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297 if ( !exists $self->{'attributes'} ) {
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298 if ( !$self->adaptor() ) {
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299 return [];
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300 }
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301
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302 my $attribute_adaptor = $self->adaptor->db->get_AttributeAdaptor();
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303 $self->{'attributes'} = $attribute_adaptor->fetch_all_by_Operon($self);
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304 }
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305
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306 if ( defined $attrib_code ) {
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307 my @results =
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308 grep { uc( $_->code() ) eq uc($attrib_code) }
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309 @{ $self->{'attributes'} };
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310 return \@results;
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311 } else {
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312 return $self->{'attributes'};
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313 }
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314 }
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315
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316 =head2 get_all_DBEntries
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317
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318 Arg [1] : (optional) String, external database name
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319
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320 Arg [2] : (optional) String, external_db type
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321
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322 Example : @dbentries = @{ $gene->get_all_DBEntries() };
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323
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324 Description: Retrieves DBEntries (xrefs) for this operon. This does
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325 *not* include DBEntries that are associated with the
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326 transcripts and corresponding translations of this
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327 gene (see get_all_DBLinks()).
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328
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329 This method will attempt to lazy-load DBEntries
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330 from a database if an adaptor is available and no
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331 DBEntries are present on the gene (i.e. they have not
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332 already been added or loaded).
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333
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334 Return type: Listref of Bio::EnsEMBL::DBEntry objects
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335 Exceptions : none
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336 Caller : get_all_DBLinks, OperonAdaptor::store
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337 Status : Stable
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338
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339 =cut
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340
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341 sub get_all_DBEntries {
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342 my ( $self, $db_name_exp, $ex_db_type ) = @_;
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343
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344 my $cache_name = 'dbentries';
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345
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346 if ( defined($db_name_exp) ) {
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347 $cache_name .= $db_name_exp;
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348 }
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349
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350 if ( defined($ex_db_type) ) {
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351 $cache_name .= $ex_db_type;
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352 }
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353
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354 # if not cached, retrieve all of the xrefs for this gene
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355 if ( !defined( $self->{$cache_name} ) && defined( $self->adaptor() ) ) {
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356 $self->{$cache_name} =
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357 $self->adaptor()->db()->get_DBEntryAdaptor()
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358 ->fetch_all_by_Operon( $self, $db_name_exp, $ex_db_type );
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359 }
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360
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361 $self->{$cache_name} ||= [];
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362
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363 return $self->{$cache_name};
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364 }
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365
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366 1;
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367
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