Mercurial > repos > dereeper > roary_plots
comparison Roary/t/Bio/Roary/Output/QueryGroups.t @ 0:c47a5f61bc9f draft
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author | dereeper |
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date | Fri, 14 May 2021 20:27:06 +0000 |
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-1:000000000000 | 0:c47a5f61bc9f |
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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 |