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comparison Roary/t/Bio/Roary/Output/QueryGroups.t @ 0:c47a5f61bc9f draft

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author dereeper
date Fri, 14 May 2021 20:27:06 +0000
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-1:000000000000 0:c47a5f61bc9f
1 #!/usr/bin/env perl
2 use strict;
3 use warnings;
4 use Data::Dumper;
5 use Moose;
6 BEGIN { unshift( @INC, './t/lib' ) }
7 with 'TestHelper';
8
9 BEGIN { unshift( @INC, './lib' ) }
10
11 BEGIN {
12 use Test::Most;
13 use_ok('Bio::Roary::Output::QueryGroups');
14 }
15
16 my $plot_groups_obj = Bio::Roary::AnalyseGroups->new(
17 fasta_files => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ],
18 groups_filename => 't/data/query_groups'
19 );
20
21 my $obj;
22 ok($obj = Bio::Roary::Output::QueryGroups->new(
23 analyse_groups => $plot_groups_obj,
24 input_filenames => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ]
25 ),'initialise groups query object');
26
27 ok($obj->groups_union(), 'create the union file');
28 ok($obj->groups_intersection(), 'create the intersection file');
29 ok($obj->groups_complement(), 'create the complement file');
30
31 compare_files('union_of_groups.gg','t/data/expected_union_of_groups.gg', 'contents of the union groups as expected');
32 compare_files('intersection_of_groups.gg', 't/data/expected_intersection_of_groups.gg', 'contents of the intersection groups as expected');
33 compare_files('complement_of_groups.gg', 't/data/expected_complement_of_groups.gg', 'contents of the complement groups as expected');
34
35 ######################################
36 # test varying core definition
37 ok($obj = Bio::Roary::Output::QueryGroups->new(
38 analyse_groups => $plot_groups_obj,
39 input_filenames => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ],
40 core_definition => 0.66
41 ),'initialise groups query object');
42
43 ok($obj->groups_intersection(), 'create the intersection file');
44 ok($obj->groups_complement(), 'create the complement file');
45
46 compare_files('intersection_of_groups.gg', 't/data/expected_intersection_of_groups_core0.66.gg', 'contents of the intersection groups as expected');
47 compare_files('complement_of_groups.gg', 't/data/expected_complement_of_groups_core0.66.gg', 'contents of the complement groups as expected');
48
49
50 unlink('union_of_groups.gg');
51 unlink('intersection_of_groups.gg');
52 unlink('complement_of_groups.gg');
53
54 ######################################
55
56 $plot_groups_obj = Bio::Roary::AnalyseGroups->new(
57 fasta_files => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ],
58 groups_filename => 't/data/query_groups_paralogs'
59 );
60
61 ok($obj = Bio::Roary::Output::QueryGroups->new(
62 analyse_groups => $plot_groups_obj,
63 input_filenames => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ]
64 ),'initialise groups query object with paralogs');
65
66 ok($obj->groups_intersection(), 'create the intersection file');
67
68 compare_files('intersection_of_groups.gg', 't/data/expected_intersection_of_groups_paralogs.gg', 'contents of the intersection groups with paralogs as expected');
69 unlink('intersection_of_groups.gg');
70
71
72 done_testing();
73