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1 package Bio::Roary::Output::DifferenceBetweenSets;
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2
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3 # ABSTRACT: Given two sets of isolates and a group file, output whats unique in each and whats in common
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4
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5 =head1 SYNOPSIS
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6
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7 Given two sets of isolates and a group file, output whats unique in each and whats in common
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8 use Bio::Roary::Output::DifferenceBetweenSets;
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9
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10 my $obj = Bio::Roary::Output::DifferenceBetweenSets->new(
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11 analyse_groups => $analyse_groups,
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12 input_filenames_sets =>
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13 [
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14 ['aaa.faa','bbb.faa'],
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15 ['ccc.faa','ddd.faa']
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16 ],
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17 );
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18 $obj->groups_set_one_unique();
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19 $obj->groups_set_two_unique();
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20 $obj->groups_in_common();
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21
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22 =cut
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23
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24 use Moose;
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25 use Bio::SeqIO;
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26 use Bio::Roary::Exceptions;
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27 use Bio::Roary::AnalyseGroups;
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28 use Bio::Roary::Output::QueryGroups;
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29
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30 has 'analyse_groups' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
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31 has 'input_filenames_sets' => ( is => 'ro', isa => 'ArrayRef[ArrayRef]', required => 1 );
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32 has 'output_filename_base' => ( is => 'ro', isa => 'Str', default => 'set_difference' );
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33
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34 has '_query_groups_objs' => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build__query_groups_objs' );
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35
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36 # TODO: update to handle more than 2 input sets
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37
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38 sub _build__query_groups_objs {
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39 my ($self) = @_;
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40 my @query_groups_objs;
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41 for my $file_name_set ( @{ $self->input_filenames_sets } ) {
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42 push(
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43 @query_groups_objs,
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44 Bio::Roary::Output::QueryGroups->new(
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45 analyse_groups => $self->analyse_groups,
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46 input_filenames => $file_name_set
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47 )
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48 );
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49 }
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50
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51 my @all_input_files = (@{ $self->input_filenames_sets->[0] },@{ $self->input_filenames_sets->[1] });
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52 push(
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53 @query_groups_objs,
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54 Bio::Roary::Output::QueryGroups->new(
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55 analyse_groups => $self->analyse_groups,
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56 input_filenames => \@all_input_files
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57 )
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58 );
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59
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60
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61 return \@query_groups_objs;
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62 }
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63
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64 sub _subtract_arrays {
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65 my ( $self, $array_1, $array_2 ) = @_;
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66 my %array_1 = map { $_ => 1 } @{$array_1};
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67 my @difference = grep { not $array_1{$_} } @{$array_2};
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68 return \@difference;
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69 }
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70
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71 sub _groups_unique {
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72 my ( $self, $output_filename, $query_group1, $query_group2 ) = @_;
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73 my $unique_groups = $self->_subtract_arrays( $query_group2->_groups, $query_group1->_groups );
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74 $query_group1->groups_with_external_inputs( $output_filename, $unique_groups );
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75 }
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76
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77 sub groups_set_one_unique_filename
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78 {
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79 my ($self) = @_;
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80 return $self->output_filename_base . '_unique_set_one';
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81 }
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82
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83 sub groups_set_two_unique_filename
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84 {
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85 my ($self) = @_;
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86 return $self->output_filename_base . '_unique_set_two';
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87 }
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88
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89 sub groups_in_common_filename
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90 {
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91 my ($self) = @_;
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92 return $self->output_filename_base . '_common_set';
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93 }
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94
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95
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96 sub groups_set_one_unique {
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97 my ($self) = @_;
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98 $self->_groups_unique(
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99 $self->groups_set_one_unique_filename,
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100 $self->_query_groups_objs->[0],
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101 $self->_query_groups_objs->[1]
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102 );
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103 }
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104
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105 sub groups_set_two_unique {
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106 my ($self) = @_;
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107 $self->_groups_unique(
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108 $self->groups_set_two_unique_filename,
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109 $self->_query_groups_objs->[1],
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110 $self->_query_groups_objs->[0]
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111 );
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112 }
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113
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114 sub groups_in_common {
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115 my ($self) = @_;
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116 my $unique_group_1 = $self->_subtract_arrays( $self->_query_groups_objs->[0]->_groups, $self->_query_groups_objs->[1]->_groups );
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117 my $unique_group_2 = $self->_subtract_arrays( $self->_query_groups_objs->[1]->_groups, $self->_query_groups_objs->[0]->_groups );
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118 my $common_groups_1 = $self->_subtract_arrays( $unique_group_1,$self->_query_groups_objs->[2]->_groups);
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119 my $common_groups_2 = $self->_subtract_arrays( $unique_group_2,$common_groups_1);
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120 $self->_query_groups_objs->[2]->groups_with_external_inputs( $self->groups_in_common_filename, $common_groups_2 );
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121 }
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122
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123 no Moose;
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124 __PACKAGE__->meta->make_immutable;
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125
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126 1;
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