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comparison Roary/lib/Bio/Roary/Output/DifferenceBetweenSets.pm @ 0:c47a5f61bc9f draft

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author dereeper
date Fri, 14 May 2021 20:27:06 +0000
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1 package Bio::Roary::Output::DifferenceBetweenSets;
2
3 # ABSTRACT: Given two sets of isolates and a group file, output whats unique in each and whats in common
4
5 =head1 SYNOPSIS
6
7 Given two sets of isolates and a group file, output whats unique in each and whats in common
8 use Bio::Roary::Output::DifferenceBetweenSets;
9
10 my $obj = Bio::Roary::Output::DifferenceBetweenSets->new(
11 analyse_groups => $analyse_groups,
12 input_filenames_sets =>
13 [
14 ['aaa.faa','bbb.faa'],
15 ['ccc.faa','ddd.faa']
16 ],
17 );
18 $obj->groups_set_one_unique();
19 $obj->groups_set_two_unique();
20 $obj->groups_in_common();
21
22 =cut
23
24 use Moose;
25 use Bio::SeqIO;
26 use Bio::Roary::Exceptions;
27 use Bio::Roary::AnalyseGroups;
28 use Bio::Roary::Output::QueryGroups;
29
30 has 'analyse_groups' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
31 has 'input_filenames_sets' => ( is => 'ro', isa => 'ArrayRef[ArrayRef]', required => 1 );
32 has 'output_filename_base' => ( is => 'ro', isa => 'Str', default => 'set_difference' );
33
34 has '_query_groups_objs' => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build__query_groups_objs' );
35
36 # TODO: update to handle more than 2 input sets
37
38 sub _build__query_groups_objs {
39 my ($self) = @_;
40 my @query_groups_objs;
41 for my $file_name_set ( @{ $self->input_filenames_sets } ) {
42 push(
43 @query_groups_objs,
44 Bio::Roary::Output::QueryGroups->new(
45 analyse_groups => $self->analyse_groups,
46 input_filenames => $file_name_set
47 )
48 );
49 }
50
51 my @all_input_files = (@{ $self->input_filenames_sets->[0] },@{ $self->input_filenames_sets->[1] });
52 push(
53 @query_groups_objs,
54 Bio::Roary::Output::QueryGroups->new(
55 analyse_groups => $self->analyse_groups,
56 input_filenames => \@all_input_files
57 )
58 );
59
60
61 return \@query_groups_objs;
62 }
63
64 sub _subtract_arrays {
65 my ( $self, $array_1, $array_2 ) = @_;
66 my %array_1 = map { $_ => 1 } @{$array_1};
67 my @difference = grep { not $array_1{$_} } @{$array_2};
68 return \@difference;
69 }
70
71 sub _groups_unique {
72 my ( $self, $output_filename, $query_group1, $query_group2 ) = @_;
73 my $unique_groups = $self->_subtract_arrays( $query_group2->_groups, $query_group1->_groups );
74 $query_group1->groups_with_external_inputs( $output_filename, $unique_groups );
75 }
76
77 sub groups_set_one_unique_filename
78 {
79 my ($self) = @_;
80 return $self->output_filename_base . '_unique_set_one';
81 }
82
83 sub groups_set_two_unique_filename
84 {
85 my ($self) = @_;
86 return $self->output_filename_base . '_unique_set_two';
87 }
88
89 sub groups_in_common_filename
90 {
91 my ($self) = @_;
92 return $self->output_filename_base . '_common_set';
93 }
94
95
96 sub groups_set_one_unique {
97 my ($self) = @_;
98 $self->_groups_unique(
99 $self->groups_set_one_unique_filename,
100 $self->_query_groups_objs->[0],
101 $self->_query_groups_objs->[1]
102 );
103 }
104
105 sub groups_set_two_unique {
106 my ($self) = @_;
107 $self->_groups_unique(
108 $self->groups_set_two_unique_filename,
109 $self->_query_groups_objs->[1],
110 $self->_query_groups_objs->[0]
111 );
112 }
113
114 sub groups_in_common {
115 my ($self) = @_;
116 my $unique_group_1 = $self->_subtract_arrays( $self->_query_groups_objs->[0]->_groups, $self->_query_groups_objs->[1]->_groups );
117 my $unique_group_2 = $self->_subtract_arrays( $self->_query_groups_objs->[1]->_groups, $self->_query_groups_objs->[0]->_groups );
118 my $common_groups_1 = $self->_subtract_arrays( $unique_group_1,$self->_query_groups_objs->[2]->_groups);
119 my $common_groups_2 = $self->_subtract_arrays( $unique_group_2,$common_groups_1);
120 $self->_query_groups_objs->[2]->groups_with_external_inputs( $self->groups_in_common_filename, $common_groups_2 );
121 }
122
123 no Moose;
124 __PACKAGE__->meta->make_immutable;
125
126 1;