Mercurial > repos > dereeper > roary_plots
comparison Roary/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t @ 0:c47a5f61bc9f draft
Uploaded
author | dereeper |
---|---|
date | Fri, 14 May 2021 20:27:06 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:c47a5f61bc9f |
---|---|
1 #!/usr/bin/env perl | |
2 use strict; | |
3 use warnings; | |
4 use Data::Dumper; | |
5 | |
6 BEGIN { unshift( @INC, './lib' ) } | |
7 $ENV{PATH} .= ":./bin"; | |
8 | |
9 BEGIN { | |
10 use Test::Most; | |
11 use_ok('Bio::Roary::ExtractCoreGenesFromSpreadsheet'); | |
12 } | |
13 | |
14 my $obj; | |
15 | |
16 ok( | |
17 $obj = Bio::Roary::ExtractCoreGenesFromSpreadsheet->new( | |
18 spreadsheet => 't/data/core_group_statistics.csv', | |
19 ), | |
20 'initalise obj' | |
21 ); | |
22 is_deeply( $obj->ordered_core_genes, [ 'argF', 'speH', 'group_5' ], 'Correct ordering' ); | |
23 is_deeply( | |
24 $obj->sample_names_to_genes, | |
25 { | |
26 'query_2' => { | |
27 '2_3' => 1, | |
28 '2_7' => 1, | |
29 '2_2' => 1 | |
30 }, | |
31 'query_1' => { | |
32 '1_6' => 1, | |
33 '1_3' => 1, | |
34 '1_2' => 1 | |
35 } | |
36 }, | |
37 'Correct of sample names to genes is correct' | |
38 ); | |
39 | |
40 ok( | |
41 $obj = Bio::Roary::ExtractCoreGenesFromSpreadsheet->new( | |
42 spreadsheet => 't/data/core_group_statistics.csv', | |
43 allow_paralogs => 1, | |
44 ), | |
45 'initalise obj where paralogs allowed' | |
46 ); | |
47 is_deeply( $obj->ordered_core_genes, [ 'argF', 'hly', 'speH', 'group_5' ], 'Correct ordering where paralogs allowed' ); | |
48 | |
49 is_deeply( | |
50 $obj->sample_names_to_genes, | |
51 { | |
52 'query_2' => { | |
53 '2_3' => 1, | |
54 '2_7' => 1, | |
55 '2_1' => 1, | |
56 '2_2' => 1 | |
57 }, | |
58 'query_1' => { | |
59 '1_6' => 1, | |
60 '1_3' => 1, | |
61 '1_1' => 1, | |
62 '1_2' => 1 | |
63 } | |
64 }, | |
65 'Correct of sample names to genes is correct where paralogs allowed' | |
66 ); | |
67 | |
68 done_testing(); |