File Coverage

lib/Bio/Roary/Output/DifferenceBetweenSets.pm
Criterion Covered Total %
statement 55 55 100.0
branch n/a
condition n/a
subroutine 15 15 100.0
pod 0 6 0.0
total 70 76 92.1


line stmt bran cond sub pod time code
1             package Bio::Roary::Output::DifferenceBetweenSets;
2             $Bio::Roary::Output::DifferenceBetweenSets::VERSION = '3.11.0';
3             # ABSTRACT: Given two sets of isolates and a group file, output whats unique in each and whats in common
4              
5              
6 2     2   447244 use Moose;
  2         12  
  2         13  
7 2     2   12277 use Bio::SeqIO;
  2         50507  
  2         50  
8 2     2   239 use Bio::Roary::Exceptions;
  2         5  
  2         39  
9 2     2   214 use Bio::Roary::AnalyseGroups;
  2         5  
  2         77  
10 2     2   421 use Bio::Roary::Output::QueryGroups;
  2         6  
  2         910  
11              
12             has 'analyse_groups' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
13             has 'input_filenames_sets' => ( is => 'ro', isa => 'ArrayRef[ArrayRef]', required => 1 );
14             has 'output_filename_base' => ( is => 'ro', isa => 'Str', default => 'set_difference' );
15              
16             has '_query_groups_objs' => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build__query_groups_objs' );
17              
18             # TODO: update to handle more than 2 input sets
19              
20             sub _build__query_groups_objs {
21 8     8   32 my ($self) = @_;
22 8         20 my @query_groups_objs;
23 8         25 for my $file_name_set ( @{ $self->input_filenames_sets } ) {
  8         255  
24 16         537 push(
25             @query_groups_objs,
26             Bio::Roary::Output::QueryGroups->new(
27             analyse_groups => $self->analyse_groups,
28             input_filenames => $file_name_set
29             )
30             );
31             }
32            
33 8         23 my @all_input_files = (@{ $self->input_filenames_sets->[0] },@{ $self->input_filenames_sets->[1] });
  8         285  
  8         227  
34 8         204 push(
35             @query_groups_objs,
36             Bio::Roary::Output::QueryGroups->new(
37             analyse_groups => $self->analyse_groups,
38             input_filenames => \@all_input_files
39             )
40             );
41            
42            
43 8         261 return \@query_groups_objs;
44             }
45              
46             sub _subtract_arrays {
47 48     48   116 my ( $self, $array_1, $array_2 ) = @_;
48 48         70 my %array_1 = map { $_ => 1 } @{$array_1};
  168         357  
  48         119  
49 48         85 my @difference = grep { not $array_1{$_} } @{$array_2};
  217         435  
  48         86  
50 48         151 return \@difference;
51             }
52              
53             sub _groups_unique {
54 16     16   55 my ( $self, $output_filename, $query_group1, $query_group2 ) = @_;
55 16         424 my $unique_groups = $self->_subtract_arrays( $query_group2->_groups, $query_group1->_groups );
56 16         95 $query_group1->groups_with_external_inputs( $output_filename, $unique_groups );
57             }
58              
59             sub groups_set_one_unique_filename
60             {
61 15     15 0 47 my ($self) = @_;
62 15         537 return $self->output_filename_base . '_unique_set_one';
63             }
64              
65             sub groups_set_two_unique_filename
66             {
67 15     15 0 32 my ($self) = @_;
68 15         477 return $self->output_filename_base . '_unique_set_two';
69             }
70              
71             sub groups_in_common_filename
72             {
73 15     15 0 38 my ($self) = @_;
74 15         391 return $self->output_filename_base . '_common_set';
75             }
76              
77              
78             sub groups_set_one_unique {
79 8     8 0 25 my ($self) = @_;
80 8         62 $self->_groups_unique(
81             $self->groups_set_one_unique_filename,
82             $self->_query_groups_objs->[0],
83             $self->_query_groups_objs->[1]
84             );
85             }
86              
87             sub groups_set_two_unique {
88 8     8 0 27 my ($self) = @_;
89 8         38 $self->_groups_unique(
90             $self->groups_set_two_unique_filename,
91             $self->_query_groups_objs->[1],
92             $self->_query_groups_objs->[0]
93             );
94             }
95              
96             sub groups_in_common {
97 8     8 0 39 my ($self) = @_;
98 8         271 my $unique_group_1 = $self->_subtract_arrays( $self->_query_groups_objs->[0]->_groups, $self->_query_groups_objs->[1]->_groups );
99 8         238 my $unique_group_2 = $self->_subtract_arrays( $self->_query_groups_objs->[1]->_groups, $self->_query_groups_objs->[0]->_groups );
100 8         205 my $common_groups_1 = $self->_subtract_arrays( $unique_group_1,$self->_query_groups_objs->[2]->_groups);
101 8         34 my $common_groups_2 = $self->_subtract_arrays( $unique_group_2,$common_groups_1);
102 8         269 $self->_query_groups_objs->[2]->groups_with_external_inputs( $self->groups_in_common_filename, $common_groups_2 );
103             }
104              
105 2     2   13 no Moose;
  2         5  
  2         12  
106             __PACKAGE__->meta->make_immutable;
107              
108             1;
109              
110             __END__
111              
112             =pod
113              
114             =encoding UTF-8
115              
116             =head1 NAME
117              
118             Bio::Roary::Output::DifferenceBetweenSets - Given two sets of isolates and a group file, output whats unique in each and whats in common
119              
120             =head1 VERSION
121              
122             version 3.11.0
123              
124             =head1 SYNOPSIS
125              
126             Given two sets of isolates and a group file, output whats unique in each and whats in common
127             use Bio::Roary::Output::DifferenceBetweenSets;
128              
129             my $obj = Bio::Roary::Output::DifferenceBetweenSets->new(
130             analyse_groups => $analyse_groups,
131             input_filenames_sets =>
132             [
133             ['aaa.faa','bbb.faa'],
134             ['ccc.faa','ddd.faa']
135             ],
136             );
137             $obj->groups_set_one_unique();
138             $obj->groups_set_two_unique();
139             $obj->groups_in_common();
140              
141             =head1 AUTHOR
142              
143             Andrew J. Page <ap13@sanger.ac.uk>
144              
145             =head1 COPYRIGHT AND LICENSE
146              
147             This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
148              
149             This is free software, licensed under:
150              
151             The GNU General Public License, Version 3, June 2007
152              
153             =cut