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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 # Ensembl module for Bio::EnsEMBL::Variation::StructuralVariation
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22 #
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23 # Copyright (c) 2004 Ensembl
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24 #
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25
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26
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27 =head1 NAME
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28
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29 Bio::EnsEMBL::Variation::StructuralVariation - Ensembl representation of a structural variation.
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30
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31 =head1 SYNOPSIS
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32
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33 # Structural variation representing a CNV
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34 $sv = Bio::EnsEMBL::Variation::StructuralVariation->new
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35 (-variation_name => 'esv25480',
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36 -class_so_term => 'structural_variant',
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37 -source => 'DGVa',
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38 -source_description => 'Database of Genomic Variants Archive',
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39 -study_name => 'estd20',
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40 -study_description => 'Conrad 2009 "Origins and functional impact of copy number variation in the human genome." PMID:19812545 [remapped from build NCBI36]',
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41 -study_url => 'ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd20_Conrad_et_al_2009',
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42 -external_reference => 'pubmed/19812545');
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43
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44 ...
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45
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46 print $sv->name(), ":", $sv->var_class();
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47
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48 =head1 DESCRIPTION
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49
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50 This is a class representing a structural variation from the
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51 ensembl-variation database. A structural variant may have a copy number variation, a tandem duplication,
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52 an inversion of the sequence or others structural variations.
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53
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54 The position of a StructuralVariation object on the Genome is represented
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55 by the <Bio::EnsEMBL::Variation::StructuralVariationFeature> class.
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56
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57 =head1 METHODS
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58
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59 =cut
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60
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61 use strict;
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62 use warnings;
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63
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64 package Bio::EnsEMBL::Variation::StructuralVariation;
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65
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66 use Bio::EnsEMBL::Variation::BaseStructuralVariation;
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67
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68 our @ISA = ('Bio::EnsEMBL::Variation::BaseStructuralVariation');
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69
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70
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71 sub new {
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72 my $caller = shift;
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73 my $class = ref($caller) || $caller;
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74
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75 my $self = Bio::EnsEMBL::Variation::BaseStructuralVariation->new(@_);
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76 return(bless($self, $class));
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77 }
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78
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79 =head2 get_all_SupportingStructuralVariants
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80
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81 Example : $sv->get_all_SupportingStructuralVariants();
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82 Description : Retrieves all SupportingStructuralVariation associated with this structural variation.
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83 Return empty list if there are none.
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84 Returntype : reference to list of Bio::EnsEMBL::Variation::SupportingStructuralVariation objects
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85 Exceptions : None
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86 Caller : general
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87 Status : At Risk
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88
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89 =cut
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90
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91 sub get_all_SupportingStructuralVariants {
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92 my $self = shift;
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93
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94 if (defined ($self->{'adaptor'})){
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95 my $ssv_adaptor = $self->{'adaptor'}->db()->get_SupportingStructuralVariationAdaptor();
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96 return $ssv_adaptor->fetch_all_by_StructuralVariation($self);
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97 }
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98 warn("No variation database attached");
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99 return [];
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100 }
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101
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102
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103 =head2 summary_as_hash
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104
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105 Example : $sv_summary = $sv->summary_as_hash();
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106 Description : Retrieves a textual summary of this StructuralVariation object.
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107 Returns : hashref of descriptive strings
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108
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109 =cut
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110
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111 sub summary_as_hash {
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112 my $self = shift;
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113 my %summary;
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114 $summary{'display_id'} = $self->display_id;
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115 $summary{'study_name'} = $self->study_name;
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116 $summary{'study_description'} = $self->study_description;
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117 $summary{'class'} = $self->var_class;
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118 return \%summary;
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119
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120 }
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121
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122 1;
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