0
|
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();
|