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1 #
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2 # Ensembl module for Bio::EnsEMBL::Funcgen::FeatureSet
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3 #
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4
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5 =head1 LICENSE
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6
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7 Copyright (c) 1999-2011 The European Bioinformatics Institute and
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8 Genome Research Limited. All rights reserved.
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9
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10 This software is distributed under a modified Apache license.
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11 For license details, please see
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12
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13 http://www.ensembl.org/info/about/code_licence.html
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14
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15 =head1 CONTACT
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16
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17 Please email comments or questions to the public Ensembl
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18 developers list at <ensembl-dev@ebi.ac.uk>.
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19
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20 Questions may also be sent to the Ensembl help desk at
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21 <helpdesk@ensembl.org>.
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22
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23
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24 =head1 NAME
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25
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26 Bio::EnsEMBL::FeatureSet - A module to represent FeatureSet.
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27
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28
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29 =head1 SYNOPSIS
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30
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31 use Bio::EnsEMBL::Funcgen::FeatureSet;
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32
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33 my $result_set = Bio::EnsEMBL::Funcgen::FeatureSet->new(
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34
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35 );
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36
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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 A FeatureSet object provides access to a set of feature predictions and their details, which may have been generated from a
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42 single or multiple Experiments with potentially differing analyses. The FeatureSet itself will only have a single analysis
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43 which may be one or a combination of programs but will be represented by one analysis record.
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44
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45 =cut
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46
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47 use strict;
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48 use warnings;
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49
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50 package Bio::EnsEMBL::Funcgen::FeatureSet;
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51
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52 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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53 use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate);
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54 use Bio::EnsEMBL::Funcgen::Set;
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55
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56 use vars qw(@ISA);
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57 @ISA = qw(Bio::EnsEMBL::Funcgen::Set);
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58
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59 my %valid_classes = ( annotated => undef,
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60 regulatory => undef,
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61 external => undef,
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62 segmentation => undef, );
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63
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64 =head2 new
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65
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66 -name => $name,
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67 -feature_type => $ftype,
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68 -cell_type => $ctype,
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69 -name => $name,
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70 -description => 'Release 3.1',
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71 -display_label => 'Short name',
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72 -analysis => $analysis,
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73 Arg [-EXPERIMENT_ID] : Experiment dbID
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74 -dbid => $dbid,
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75 Arg [-ADAPTOR]
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76
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77 Example : my $feature = Bio::EnsEMBL::Funcgen::FeatureSet->new(
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78 -dbid => $dbid,
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79 -analysis => $analysis,
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80 -feature_type => $ftype,
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81 -cell_type => $ctype,
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82 -name => $name,
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83 -feature_class => 'annotated',
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84 -description => 'Release 3.1',
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85 -display_label => 'Short name',
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86 -input_set => $iset,
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87 );
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88 Description: Constructor for FeatureSet objects.
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89 Returntype : Bio::EnsEMBL::Funcgen::FeatureSet
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90 Exceptions : Throws if FeatureType defined
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91 Caller : General
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92 Status : At risk
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93
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94 =cut
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95
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96 sub new {
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97 my $caller = shift;
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98 my $class = ref($caller) || $caller;
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99 my $self = $class->SUPER::new(@_);
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100
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101 my ( $desc, $dlabel, $iset_id, $iset, $exp_id, $exp ) =
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102 rearrange( [
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103 'DESCRIPTION', 'DISPLAY_LABEL',
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104 'INPUT_SET_ID', 'INPUT_SET', 'EXPERIMENT_ID', 'EXPERIMENT'
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105 ],
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106 @_ );
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107
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108
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109 if($exp_id || $exp){
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110 throw('Passing an Experiment or an experiment_id is now deprecated,'.
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111 ' please use -input_set or -input_set_id instead');
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112 }
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113
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114 #Allow exp or exp_id to be passed to support storing and lazy loading
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115
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116 #Mandatory params checks here (setting done in Set.pm)
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117 throw('Must provide a FeatureType')
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118 if ( !defined $self->feature_type );
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119
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120 #explicit type check here to avoid invalid types being imported as NULL
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121 #subsequently throwing errors on retrieval
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122 my $type = $self->feature_class;
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123
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124 if ( !( $type && exists $valid_classes{$type} ) ) {
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125 throw( 'You must define a valid FeatureSet type e.g. ' .
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126 join( ', ', keys %valid_classes ) );
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127 }
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128
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129 #Direct assignment to prevent need for set arg test in method
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130
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131 $self->{'description'} = $desc if defined $desc;
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132 $self->{'display_label'} = $dlabel if defined $dlabel;
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133 $self->{'input_set_id'} = $iset_id if defined $iset_id;
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134
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135 if ( defined $iset ) {
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136 #Exp obj is only passed during object storing
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137 #so let the adaptor do is_stored_and_valid
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138 $self->{'input_set'} = $iset;
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139 }
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140
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141 return $self;
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142 } ## end sub new
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143
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144
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145
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146 =head2 new_fast
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147
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148 Args : Hashref with all internal attributes set
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149 Example : none
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150 Description: Quick and dirty version of new. Only works if the code is very
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151 disciplined.
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152 Returntype : Bio::EnsEMBL::Funcgen::FeatureSet
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153 Exceptions : None
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154 Caller : General
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155 Status : At Risk
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156
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157 =cut
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158
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159
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160 sub new_fast {
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161 return bless ($_[1], $_[0]);
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162 }
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163
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164
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165 =head2 description
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166
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167 Example : print "Feature set description is:\t".$fset->description."\n";
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168 Description: Getter for the description of this FeatureSet. e.g. Release 3.1
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169 Returntype : String
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170 Exceptions : None
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171 Caller : General
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172 Status : At Risk
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173
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174 =cut
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175
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176 sub description {
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177 return $_[0]->{'description'};
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178 }
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179
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180
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181
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182 =head2 display_label
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183
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184 Example : print $rset->display_label;
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185 Description: Getter for the display_label attribute for this FeatureSet.
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186 Returntype : String
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187 Exceptions : None
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188 Caller : General
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189 Status : At Risk
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190
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191 =cut
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192
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193 sub display_label {
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194 my $self = shift;
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195
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196 if ( !$self->{'display_label'} ) {
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197
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198 if ( $self->feature_type->class() eq 'Regulatory Feature' ) {
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199 $self->{'display_label'} = $self->name;
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200 }
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201 else {
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202 #This still fails here if we don't have a class or a cell_type set
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203
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204 $self->{'display_label'} =
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205 $self->feature_type->name() . " - " . $self->cell_type->name() .
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206 " Enriched Sites";
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207 }
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208 }
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209
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210 return $self->{'display_label'};
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211 }
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212
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213
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214
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215
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216 =head2 get_FeatureAdaptor
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217
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218 Example :
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219 Description: Retrieves and caches FeatureAdaptor of feature_set type
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220 Returntype : Bio::EnsEMBL::Funcgen::DBSQL::ucfirst($self->feature_class())FeatureAdaptor
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221 Exceptions : None
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222 Caller : General
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223 Status : At Risk
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224
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225 =cut
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226
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227
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228 sub get_FeatureAdaptor{
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229 my $self = shift;
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230
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231 if(! exists $self->{'adaptor_refs'}){
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232
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233 foreach my $valid_class(keys %valid_classes){
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234 my $method = 'get_'.ucfirst($valid_class).'FeatureAdaptor';
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235
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236 $self->{'adaptor_refs'}{$valid_class} = $self->adaptor->db->$method;
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237 }
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238 }
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239
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240 return $self->{'adaptor_refs'}->{$self->feature_class()};
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241
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242 }
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243
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244
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245
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246 =head2 get_Features_by_Slice
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247
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248 Example : my @features = @{$FeatureSet->get_Features_by_Slice($slice)};
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249 Description: Retrieves all Features for this FeatureSet for a given Slice
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250 Returntype : ARRAYREF containing Features of the feature_set type i.e. Annotated, Regulatory or Supporting;
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251 Exceptions : None
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252 Caller : General
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253 Status : At Risk
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254
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255 =cut
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256
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257 sub get_Features_by_Slice{
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258 my ($self, $slice) = @_;
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259
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260 return $self->get_FeatureAdaptor->fetch_all_by_Slice_FeatureSets($slice, [$self]);
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261 }
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262
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263
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264 =head2 get_Features_by_FeatureType
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265
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266 Arg[0] : Bio::EnsEMBL::Funcgen::FeatureType
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267 Example : my @features = @{$FeatureSet->get_Features_by_FeatureType($ftype)};
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268 Description: Retrieves all Features for this FeatureSet for a given FeatureType
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269 or associated FeatureType. This is mainly used by external FeatureSets
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270 which can sometimes have more than one associated FeatureType.
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271 Returntype : ARRAYREF
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272 Exceptions : None
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273 Caller : General
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274 Status : At Risk
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275
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276 =cut
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277
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278
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279 sub get_Features_by_FeatureType{
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280 my ($self, $type) = @_;
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281
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282 return $self->get_FeatureAdaptor->fetch_all_by_FeatureType_FeatureSets($type, [$self]);
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283 }
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284
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285
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286 =head2 get_all_Features
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287
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288 Example : my @features = @{$FeatureSet->get_all_Features};
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289 Description: Retrieves all Features for this FeatureSet
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290 Returntype : ARRAYREF
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291 Exceptions : None
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292 Caller : General
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293 Status : At Risk
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294
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295 =cut
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296
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297 sub get_all_Features{
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298 my $self = shift;
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299
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300 return $self->get_FeatureAdaptor->fetch_all_by_FeatureSets([$self]);
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301 }
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302
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303
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304
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305
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306 =head2 is_focus_set
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307
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308 Args : None
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309 Example : if($fset->is_focus_set){ ... }
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310 Description: Returns true if FeatureSet is a focus set used in the RegulatoryBuild
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311 Returntype : Boolean
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312 Exceptions : Throws if meta entry not present
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313 Caller : General
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314 Status : At Risk
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315
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316 =cut
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317
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318 sub is_focus_set{
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319 my $self = shift;
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320
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321 if(! defined $self->{focus_set}){
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322
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323 if(! defined $self->cell_type){
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324 warn "FeatureSet without an associated CellType cannot be a focus set:\t".$self->name;
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325 $self->{focus_set} = 0;
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326 }
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327 else{
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328 $self->{focus_set} = $self->adaptor->fetch_focus_set_config_by_FeatureSet($self);
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329 }
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330 }
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331
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332 return $self->{focus_set};
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333 }
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334
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335
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336 =head2 is_attribute_set
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337
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338 Args : None
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339 Example : if($fset->is_attribute_set){ ... }
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340 Description: Returns true if FeatureSet is a supporting/attribute(focus or not) set used in the RegulatoryBuild
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341 Returntype : Boolean
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342 Exceptions : Throws if meta entry not present
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343 Caller : General
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344 Status : At Risk
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345
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346 =cut
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347
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348 sub is_attribute_set{
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349 my $self = shift;
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350
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351 if(! defined $self->{attribute_set}){
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352
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353 if(! defined $self->cell_type){
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354 warn "FeatureSet without an associated CellType cannot be a attribute set:\t".$self->name;
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355 $self->{attribute_set} = 0;
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356 }
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357 else{
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358 $self->{attribute_set} = $self->adaptor->fetch_attribute_set_config_by_FeatureSet($self);
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359 }
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360 }
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361
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362 return $self->{attribute_set};
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363 }
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364
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365
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366 =head2 get_InputSet
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367
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368 Example : my $input_set = $FeatureSet->get_InputSet;
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369 Description: Retrieves the InputSet for this FeatureSet
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370 Returntype : Bio::EnsEMBL::Funcgen::InputSet
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371 Exceptions : None
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372 Caller : General
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373 Status : At Risk
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374
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375 =cut
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376
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377 sub get_InputSet{
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378 my $self = shift;
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379
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380 if( (! defined $self->{input_set}) &&
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381 (defined $self->{input_set_id}) ){
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382 $self->{input_set} = $self->adaptor->db->get_InputSetAdaptor->fetch_by_dbID($self->{input_set_id});
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383 }
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384
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385 return $self->{input_set};
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386 }
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387
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388
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389
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390 =head2 source_label
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391
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392 Example : my $source_label = $fset->source_label;
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393 Description: Retrieves the source label this FeatureSet, used in zmenus
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394 Returntype : Arrayref of Strings
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395 Exceptions : None
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396 Caller : Webcode zmenus
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397 Status : At Risk - remove, to be done by webcode?
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398
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399 =cut
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400
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401 #These are used to link through to the experiment view based on feature_set_id
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402
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403 sub source_label{
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404 my $self = shift;
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405
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406 if (! defined $self->{source_label}) {
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407 my $input_set = $self->get_InputSet;
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408 my @source_labels;
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409
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410 if ($input_set) {
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411
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412
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413 foreach my $isset(@{$input_set->get_InputSubsets}){
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414
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415 if(defined $isset->archive_id){
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416 push @source_labels, $isset->archive_id;
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417 }
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418 #Archive IDs e.g. SRX identifiers or undef.
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419 }
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420
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421 #Append project name
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422 my $exp_group = $input_set->get_Experiment->experimental_group;
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423
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424 if ($exp_group &&
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425 $exp_group->is_project) {
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426 push @source_labels, $exp_group->name;
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427 }
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428 }
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429
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430
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431 $self->{source_label} = join(' ', @source_labels);
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432 }
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433
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434 return $self->{source_label};
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435 }
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436
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437
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438
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439
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440 ### DEPRECATED ###
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441
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442 =head2 get_Experiment
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443 #
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444 # Example : my $exp = $FeatureSet->get_Experiment;
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445 # Description: Retrieves the Experiment for this FeatureSet
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446 # Returntype : Bio::EnsEMBL::Funcgen::Experiment
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447 # Exceptions : None
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448 # Caller : General
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449 Status : DEPRECATED
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450
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451 =cut
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452
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453 sub get_Experiment{
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454 throw('FeatureSet::get_Experiment is not longer supported, please use FeatureSet::get_InputSet');
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455 }
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456
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457
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458 1;
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