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1 #
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2 # Ensembl module for Bio::EnsEMBL::Funcgen::SegmentationFeature
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3 #
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4 # You may distribute this module under the same terms as Perl itself
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5
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6 =head1 LICENSE
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7
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8 Copyright (c) 1999-2011 The European Bioinformatics Institute and
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9 Genome Research Limited. All rights reserved.
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10
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11 This software is distributed under a modified Apache license.
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12 For license details, please see
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13
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14 http://www.ensembl.org/info/about/code_licence.html
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15
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16 =head1 CONTACT
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17
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18 Please email comments or questions to the public Ensembl
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19 developers list at <ensembl-dev@ebi.ac.uk>.
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20
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21 Questions may also be sent to the Ensembl help desk at
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22 <helpdesk@ensembl.org>.
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23
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24
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25 =head1 NAME
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26
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27 Bio::EnsEMBL::SegmentationFeature - Genomic segmentation feature
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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::SegmentationFeature;
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32
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33 my $feature = Bio::EnsEMBL::Funcgen::SegmentationFeature->new(
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34 -SLICE => $chr_1_slice,
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35 -START => 1_000_000,
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36 -END => 1_000_024,
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37 -STRAND => 0,
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38 -FEATURE_SET => $fset,
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39 -FEATURE_TYPE => $ftype,
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40 );
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41
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42
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43
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44 =head1 DESCRIPTION
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45
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46 An SegmentationFeature object represents the genomic placement of a prediction
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47 generated by the eFG analysis pipeline. This normally represents the
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48 output of a peak calling analysis. It can have a score and/or a summit, the
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49 meaning of which depend on the specific Analysis used to infer the feature.
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50 For example, in the case of a feature derived from a peak call over a ChIP-seq
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51 experiment, the score is the peak caller score, and summit is the point in the
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52 feature where more reads align with the genome.
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53
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54 =head1 SEE ALSO
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55
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56 Bio::EnsEMBL::Funcgen::DBSQL::SegmentationFeatureAdaptor
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57
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58 =cut
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59
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60 use strict;
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61 use warnings;
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62
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63 package Bio::EnsEMBL::Funcgen::SegmentationFeature;
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64
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65 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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66 use Bio::EnsEMBL::Utils::Exception qw( throw );
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67 use Bio::EnsEMBL::Funcgen::SetFeature;
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68
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69 use vars qw(@ISA);
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70 @ISA = qw(Bio::EnsEMBL::Funcgen::SetFeature);
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71
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72 =head2 new
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73
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74 Arg [-SLICE] : Bio::EnsEMBL::Slice - The slice on which this feature is.
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75 Arg [-START] : int - The start coordinate of this feature relative to the start of
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76 the slice it is sitting on. Coordinates start at 1 and are inclusive.
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77 Arg [-END] : int -The end coordinate of this feature relative to the start of
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78 the slice it is sitting on. Coordinates start at 1 and are inclusive.
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79 Arg [-STRAND] : int - The orientation of this feature. Valid values are 1, -1 and 0.
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80 Arg [-FEATURE_SET] : Bio::EnsEMBL::Funcgen::FeatureSet
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81 Arg [-FEATURE_TYPE] : Bio::Ensembl::Funcgen::FeatureType
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82 Arg [-DISPLAY_LABEL]: optional string - Display label for this feature
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83 Arg [-SCORE] : optional int - Score assigned by analysis pipeline
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84 Arg [-dbID] : optional int - Internal database ID.
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85 Arg [-ADAPTOR] : optional Bio::EnsEMBL::DBSQL::BaseAdaptor - Database adaptor.
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86
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87 Example : my $feature = Bio::EnsEMBL::Funcgen::SegmentationFeature->new
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88 (
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89 -SLICE => $chr_1_slice,
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90 -START => 1_000_000,
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91 -END => 1_000_024,
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92 -STRAND => -1,
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93 -FEATURE_SET => $fset,
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94 -FEATURE_TYPE => $ftype,
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95 -DISPLAY_LABEL => $text,
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96 -SCORE => $score,
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97 );
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98
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99
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100 Description: Constructor for SegmentationFeature objects.
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101 Returntype : Bio::EnsEMBL::Funcgen::SegmentationFeature
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102 Exceptions : None
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103 Caller : General
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104 Status : Medium Risk
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105
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106 =cut
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107
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108 sub new {
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109 my $caller = shift;
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110
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111 my $class = ref($caller) || $caller;
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112 my $self = $class->SUPER::new(@_);
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113 #Hard code strand => 0 here? And remove from input params?
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114 my ($score, $ftype) = rearrange(['SCORE', 'FEATURE_TYPE'], @_);
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115
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116 #test ftype as SetFeature method defaults to feature_set->feature_type
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117 throw('You must pass a valid FeatureType') if ! defined $ftype;
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118
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119 $self->{score} = $score if $score;
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120 $self->{feature_type} = $ftype;
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121
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122 return $self;
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123 }
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124
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125
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126 =head2 score
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127
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128 Arg [1] : (optional) int - score
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129 Example : my $score = $feature->score();
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130 Description: Getter and setter for the score attribute for this feature.
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131 Returntype : int
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132 Exceptions : None
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133 Caller : General
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134 Status : At Risk
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135
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136 =cut
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137
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138 sub score {
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139 my $self = shift;
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140 return $self->{'score'};
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141 }
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142
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143
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144 =head2 display_label
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145
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146 Example : my $label = $feature->display_label();
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147 Description: Getter for the display label of this feature.
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148 Returntype : String
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149 Exceptions : None
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150 Caller : General
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151 Status : At Risk
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152
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153 =cut
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154
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155 sub display_label {
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156 my $self = shift;
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157
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158 if(! $self->{'display_label'} && $self->adaptor){
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159 $self->{'display_label'} = $self->feature_type->name()." -";
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160 $self->{'display_label'} .= " ".$self->cell_type->name();
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161 }
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162
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163 return $self->{'display_label'};
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164 }
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165
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166
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167 1;
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168
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