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comparison Roary/t/Bio/Roary/GroupStatistics.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 Test::Files;
6
7 BEGIN { unshift( @INC, './lib' ) }
8 $ENV{PATH} .= ":./bin";
9
10 BEGIN {
11 use Test::Most;
12 use_ok('Bio::Roary::GroupStatistics');
13 }
14
15 my $annotate_groups = Bio::Roary::AnnotateGroups->new(
16 gff_files => ['t/data/query_1.gff','t/data/query_2.gff','t/data/query_3.gff'],
17 groups_filename => 't/data/query_groups',
18 );
19
20 my $analyse_groups = Bio::Roary::AnalyseGroups->new(
21 fasta_files => ['t/data/query_1.fa','t/data/query_2.fa','t/data/query_3.fa'],
22 groups_filename => 't/data/query_groups'
23 );
24
25 my $obj;
26
27 ok($obj = Bio::Roary::GroupStatistics->new(
28 annotate_groups_obj => $annotate_groups,
29 analyse_groups_obj => $analyse_groups
30 ),'Initialise group statistics object');
31 ok($obj->create_spreadsheet,'Create the CSV file');
32 ok(-e 'gene_presence_absence.csv', 'CSV file exists');
33 compare_ok('gene_presence_absence.csv','t/data/expected_group_statitics.csv', 'Spreadsheet content as expected');
34 ok($obj->create_rtab,'Create the Rtab file');
35 ok(-e 'gene_presence_absence.Rtab', 'Rtab file exists');
36 compare_ok('gene_presence_absence.Rtab','t/data/expected_gene_presence_and_absence.Rtab', 'Rtab matrix content as expected');
37
38 unlink('gene_presence_absence.csv');
39 unlink('gene_presence_absence.Rtab');
40
41 ############################
42
43 my $annotate_groups_2 = Bio::Roary::AnnotateGroups->new(
44 gff_files => ['t/data/query_1.gff','t/data/query_2.gff','t/data/query_3.gff','t/data/query_4_missing_genes.gff'],
45 groups_filename => 't/data/query_groups_missing_genes',
46 );
47
48 my $analyse_groups_2 = Bio::Roary::AnalyseGroups->new(
49 fasta_files => ['t/data/query_1.fa','t/data/query_2.fa','t/data/query_3.fa','t/data/query_4_missing_genes.fa'],
50 groups_filename => 't/data/query_groups_missing_genes'
51 );
52
53 ok($obj = Bio::Roary::GroupStatistics->new(
54 annotate_groups_obj => $annotate_groups_2,
55 analyse_groups_obj => $analyse_groups_2,
56 output_filename => 'missing_genes_stats.csv'
57 ),'Initialise group statistics object where one isolate has only 1 gene');
58 ok($obj->create_spreadsheet,'Create the CSV file');
59 ok(-e 'missing_genes_stats.csv', 'CSV file exists');
60 compare_ok('missing_genes_stats.csv','t/data/expected_group_statitics_missing_genes.csv', 'Spreadsheet content as expected with missing genes');
61
62 unlink('missing_genes_stats.csv');
63
64
65 ## TEST VERBOSE STATS ##
66
67 ok($obj = Bio::Roary::GroupStatistics->new(
68 annotate_groups_obj => $annotate_groups,
69 analyse_groups_obj => $analyse_groups,
70 _verbose => 1,
71 output_filename => 'verbose_stats.csv'
72 ),'Initialise group statistics object');
73 ok($obj->create_spreadsheet,'Create the CSV file');
74 ok(-e 'verbose_stats.csv', 'CSV file exists');
75 compare_ok('verbose_stats.csv','t/data/expected_group_statitics_verbose.csv', 'Verbose spreadsheet content as expected');
76
77 unlink('verbose_stats.csv');
78
79 done_testing();