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1 #
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2 # Ensembl module for Bio::EnsEMBL::Funcgen::InputSet
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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 =head1 NAME
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24
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25 Bio::EnsEMBL::InputSet - A module to represent InputSet object.
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26
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27
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28 =head1 SYNOPSIS
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29
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30 use Bio::EnsEMBL::Funcgen::InputSet;
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31
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32 #Create an InputSet
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33
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34 my $inp_set = Bio::EnsEMBL::Funcgen::InputSet->new
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35 (
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36 -DBID => $dbID,
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37 -ADAPTOR => $self,
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38 -EXPERIMENT => $exp,
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39 -FEATURE_TYPE => $ftype,
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40 -CELL_TYPE => $ctype,
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41 -FORMAT => 'READ_FORMAT',
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42 -VENDOR => 'SOLEXA',
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43 -NAME => 'ExpSet1',
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44 -REPLICATE => 1,
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45 );
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46
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47 # Add some InputSubsets
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48
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49 $inp_set->add_new_subsets($subset_name, $
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50
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51
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52
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53
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54 =head1 DESCRIPTION
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55
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56 An InputSet object provides a generic container for any non-array based feature import,
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57 allowing tracking of file import via the status table and integration into Data and FeatureSets to
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58 provide traceability to the source experiment from a given FeatureSet.
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59
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60 =cut
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61
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62 use strict;
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63 use warnings;
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64
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65 package Bio::EnsEMBL::Funcgen::InputSet;
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66
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67 use Bio::EnsEMBL::Funcgen::InputSubset;
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68 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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69 use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate);
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70 use Bio::EnsEMBL::Funcgen::Set;
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71 use Bio::EnsEMBL::Analysis;
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72
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73 use vars qw(@ISA);
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74 @ISA = qw(Bio::EnsEMBL::Funcgen::Set);
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75
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76
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77 =head2 new
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78
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79
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80
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81 Example : my $eset = Bio::EnsEMBL::Funcgen::InputSet->new(
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82 -EXPERIMENT => $exp,
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83 -FEATURE_TYPE => $ftype,
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84 -CELL_TYPE => $ctype,
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85 -FORMAT => 'READ_FORMAT',
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86 -VENDOR => 'SOLEXA',
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87 -NAME => 'ExpSet1',
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88 -ANALYSIS => $anal,
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89 -FEATURE_CLASS => 'annotated',
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90 );
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91
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92 Do we want to define subsets likes this or are we more likely to add them one by one?
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93
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94 Description: Constructor for InputSet objects.
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95 Returntype : Bio::EnsEMBL::Funcgen::InputSet
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96 Exceptions : Throws if no Experiment defined
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97 Throws if CellType or FeatureType are not valid or stored
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98 Caller : General
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99 Status : At risk
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100
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101 =cut
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102
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103 sub new {
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104 my $caller = shift;
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105
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106 my $class = ref($caller) || $caller;
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107
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108 #Add set_type here to overwrite default ref parsing in Set::set_type
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109 #This need to stay like this until we patch the DB
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110 my $self = $class->SUPER::new(@_);
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111
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112 my ($exp, $format, $vendor, $rep)
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113 = rearrange(['EXPERIMENT', 'FORMAT', 'VENDOR', 'REPLICATE'], @_);
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114
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115 if (! (ref $exp && $exp->isa('Bio::EnsEMBL::Funcgen::Experiment') && $exp->dbID())){
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116 throw('Must specify a valid stored Bio::EnsEMBL::Funcgen::Experiment');
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117 }
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118
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119
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120 #These are set in Set, just validate here
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121 throw ('Must provide a FeatureType') if(! defined $self->feature_type);
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122 throw ('Must provide a CellType') if(! defined $self->cell_type);
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123
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124 my $type = $self->feature_class;
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125
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126 #Need to move these types to config
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127
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128 if(! ($type && grep /^${type}$/, ('annotated', 'result', 'segmentation'))){
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129 throw("You must define a valid InputSet feature_class e.g. 'annotated' or 'result'");
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130 }
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131
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132 if(($type eq 'result') &&
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133 ($format ne 'SEQUENCING')){
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134 throw('InputSet does not yet support a result type InputSet which does not have the \'SEQUENCING\' format');
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135
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136 }
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137
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138
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139 #if(! defined $self->analysis){
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140 ##default analysis hack for v47
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141 ##Set directly to avoid dbID boolean check
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142 #This is to support supporting_set cache in data_set?
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143 $self->{'analysis'} = Bio::EnsEMBL::Analysis->new
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144 (-logic_name => 'external',
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145 -id => 0,#??someone needs to rewrite analysis
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146 );
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147
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148 #Change to direct setting for speed
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149 $self->{format} = $format;
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150 $self->{vendor} = $vendor;
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151 $self->{replicate} = $rep;
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152 $self->{experiment} = $exp;
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153 $self->{subsets} = {};
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154
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155 return $self;
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156 }
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157
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158
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159 =head2 add_new_subset
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160
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161 Arg [1] : string - sub set name e.g. the file name (not path as we're restricted to 30 chars)
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162 Arg [2] : Bio::EnsEMBL::Funcgen::InputSubset - optional
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163 If not defined will create a sparse InputSubset based on the name
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164 Example : $expset->add_new_subset($ss_name, $exp_subset);
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165 Description: Adds input_subset
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166 Returntype : none
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167 Exceptions : Throws if set is already present
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168 Throws if InputSubset is not valid or stored
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169 Caller : General
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170 Status : At Risk
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171
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172 =cut
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173
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174 #Do we still use the optional subset function?
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175
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176 sub add_new_subset {
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177 my ($self, $ss_name, $exp_sset) = @_;
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178
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179 #Need to test $ss_name here
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180 if(! ($ss_name && ref(\$ss_name) eq 'SCALAR')){#ref($exp_sset) would be 'REF'
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181 throw('You must pass a InputSubset name');
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182 }
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183
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184 if($self->get_subset_by_name($ss_name)){
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185 throw("Subset $ss_name is already present in this InputSet, maybe you need to alter the filename?");
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186 }
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187
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188 if(defined $exp_sset){
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189
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190 if(!(ref($exp_sset) && $exp_sset->isa('Bio::EnsEMBL::Funcgen::InputSubset') && $exp_sset->dbID())){
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191 throw('InputSubsets must be valid and stored');
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192 }
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193 }
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194 else{
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195
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196 $exp_sset = Bio::EnsEMBL::Funcgen::InputSubset->new(
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197 -name => $ss_name,
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198 -input_set => $self,
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199 );
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200 }
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201
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202 $self->{subsets}{$ss_name} = $exp_sset;
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203
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204 return $self->{subsets}{$ss_name};
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205 }
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206
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207
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208 =head2 get_Experiment
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209
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210 Example : my $exp = $exp_set->get_Experiment();
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211 Description: Getter for the Experiment of this DataSet.
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212 Returntype : Bio::EnsEMBL::Fuuncgen::Experiment
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213 Exceptions : None
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214 Caller : General
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215 Status : At Risk
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216
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217 =cut
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218
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219 sub get_Experiment{ return $_[0]->{experiment}; }
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220
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221
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222 =head2 get_InputSubsets
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223
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224 Example : my @subsets = @{$exp_set->get_InputSubsets()};
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225 Description: Getter for the InputSubsets for this InputSet.
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226 Returntype : Arrayref
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227 Exceptions : None
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228 Caller : General
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229 Status : At Risk
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230
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231 =cut
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232
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233 sub get_InputSubsets{
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234 my ($self) = shift;
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235
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236 return [ values %{$self->{'subsets'}} ];
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237 }
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238
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239
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240
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241
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242 =head2 get_subset_by_name
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243
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244 Example : my $subsets = $exp_set->get_subset_by_name('subset1');
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245 Description: Getter for the subset of a given name for this InputSet.
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246 Returntype : Bio::EnsEMBL::Funcgen::InputSubset
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247 Exceptions : None
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248 Caller : General
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249 Status : At Risk
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250
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251 =cut
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252
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253 sub get_subset_by_name{
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254 my ($self, $name) = @_;
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255 return (exists $self->{'subsets'}{$name}) ? $self->{'subsets'}{$name} : undef;
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256 }
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257
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258
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259 =head2 get_subset_names
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260
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261 Example : my @subset_names = @{$exp_set->get_subset_names()};
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262 Description: Getter for the subset names for this InputSet.
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263 Returntype : Arrayref
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264 Exceptions : None
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265 Caller : General
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266 Status : At Risk
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267
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268 =cut
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269
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270 sub get_subset_names{
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271 my ($self) = shift;
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272 return [ keys %{$self->{'subsets'}} ];
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273 }
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274
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275
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276
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277
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278 =head2 vendor
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279
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280 Arg[1] : String - vendor e.g. ILLUMINA
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281 Example : my $iset_vendor = $iset->vendor;
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282 Description: Getter for the vendor attribute of this InputSet.
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283 Returntype : String
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284 Exceptions : None
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285 Caller : General
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286 Status : At Risk
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287
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288 =cut
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289
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290 sub vendor { return $_[0]->{vendor}; }
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291
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292
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293 =head2 format
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294
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295 Arg[1] : string - format i.e. product type/format
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296 Example : my $iset_format = $iset->format;
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297 Description: Getter for the format attribute of this InputSet.
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298 Returntype : String
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299 Exceptions : None
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300 Caller : General
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301 Status : At Risk
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302
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303 =cut
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304
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305 sub format { return $_[0]->{format}; }
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306
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307
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308 =head2 replicate
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309
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310 Arg[1] : Integer - replicate 0 = merged or NA, >0 refers to individual replicate
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311 Example : if($iset->replicate){ #Do something replicate specific in here }
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312 Description: Getter for the replicate attribute of this InputSet.
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313 Returntype : Integer
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314 Exceptions : None
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315 Caller : General
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316 Status : At Risk
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317
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318 =cut
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319
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320 sub replicate { return $_[0]->{replicate}; }
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321
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322
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323
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324 =head2 source_info
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325
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326 Example : my $source_info = $input_set->source_info;
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327 Description: Getter for the experiment source info i.e. [ $label, $url ]
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328 Returntype : Listref
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329 Exceptions : None
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330 Caller : General
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331 Status : At risk
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332
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333 =cut
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334
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335 #Currently handling redundant/absent InputSubset data
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336
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337 sub source_info{
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338 my $self = shift;
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339
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340 if(! defined $self->{source_info}){
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341 #could have data_url as highest priority here
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342 #but we need to ensure removal when adding archive ids
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343 #so we link to the archive and not the old data url
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344
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345 my $exp_group = $self->get_Experiment->experimental_group;
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346 my %source_info; #Handles redundant InputSubsets
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347 my ($proj_name, $proj_link, $source_label, $source_link);
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348
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349 if($exp_group->is_project){
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350 $proj_name = $exp_group->name;
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351 $proj_link = $exp_group->url;
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352 }
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353
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354 foreach my $isset(@{$self->get_InputSubsets}){
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355
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356 if(defined $isset->archive_id ){
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357 $source_label = $isset->archive_id;
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358
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359 if(! exists $source_info{$source_label}){
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360 $source_info{$source_label} = [$source_label, undef];
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361 #source_link can is undef here as archive_id overrides display url
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362 #undef links will automatically go to the SRA
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363 }
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364 }
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365 elsif(defined $proj_name){
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366 #$source_label = $self->experimental_group->name;
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367 $source_link = $isset->display_url || $proj_link;
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368
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369 if(! exists $source_info{$source_link}){
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370 $source_info{$source_link} = [$proj_name, $source_link];
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371 }
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372 }
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373 }
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374
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375 $self->{source_info} = [values %source_info];
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376 }
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377
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378 return $self->{source_info};
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379 }
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380
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381
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382
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383 1;
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384
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