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