--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/t/Bio/Roary/GroupStatistics.t	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,79 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Data::Dumper;
+use Test::Files;
+
+BEGIN { unshift( @INC, './lib' ) }
+$ENV{PATH} .= ":./bin";
+
+BEGIN {
+    use Test::Most;
+    use_ok('Bio::Roary::GroupStatistics');
+}
+
+my $annotate_groups = Bio::Roary::AnnotateGroups->new(
+  gff_files   => ['t/data/query_1.gff','t/data/query_2.gff','t/data/query_3.gff'],
+  groups_filename => 't/data/query_groups',
+);
+
+my $analyse_groups = Bio::Roary::AnalyseGroups->new(
+    fasta_files     => ['t/data/query_1.fa','t/data/query_2.fa','t/data/query_3.fa'],
+    groups_filename => 't/data/query_groups'
+);
+
+my $obj;
+
+ok($obj = Bio::Roary::GroupStatistics->new(
+  annotate_groups_obj => $annotate_groups,
+  analyse_groups_obj  => $analyse_groups 
+),'Initialise group statistics object');
+ok($obj->create_spreadsheet,'Create the CSV file');
+ok(-e 'gene_presence_absence.csv', 'CSV file exists');
+compare_ok('gene_presence_absence.csv','t/data/expected_group_statitics.csv', 'Spreadsheet content as expected');
+ok($obj->create_rtab,'Create the Rtab file');
+ok(-e 'gene_presence_absence.Rtab', 'Rtab file exists');
+compare_ok('gene_presence_absence.Rtab','t/data/expected_gene_presence_and_absence.Rtab', 'Rtab matrix content as expected');
+
+unlink('gene_presence_absence.csv');
+unlink('gene_presence_absence.Rtab');
+
+############################
+
+my $annotate_groups_2 = Bio::Roary::AnnotateGroups->new(
+  gff_files   => ['t/data/query_1.gff','t/data/query_2.gff','t/data/query_3.gff','t/data/query_4_missing_genes.gff'],
+  groups_filename => 't/data/query_groups_missing_genes',
+);
+
+my $analyse_groups_2 = Bio::Roary::AnalyseGroups->new(
+    fasta_files     => ['t/data/query_1.fa','t/data/query_2.fa','t/data/query_3.fa','t/data/query_4_missing_genes.fa'],
+    groups_filename => 't/data/query_groups_missing_genes'
+);
+
+ok($obj = Bio::Roary::GroupStatistics->new(
+  annotate_groups_obj => $annotate_groups_2,
+  analyse_groups_obj  => $analyse_groups_2,
+  output_filename     => 'missing_genes_stats.csv' 
+),'Initialise group statistics object where one isolate has only 1 gene');
+ok($obj->create_spreadsheet,'Create the CSV file');
+ok(-e 'missing_genes_stats.csv', 'CSV file exists');
+compare_ok('missing_genes_stats.csv','t/data/expected_group_statitics_missing_genes.csv', 'Spreadsheet content as expected with missing genes');
+
+unlink('missing_genes_stats.csv');
+
+
+## TEST VERBOSE STATS ##
+
+ok($obj = Bio::Roary::GroupStatistics->new(
+  annotate_groups_obj => $annotate_groups,
+  analyse_groups_obj  => $analyse_groups,
+  _verbose            => 1,
+  output_filename     => 'verbose_stats.csv'
+),'Initialise group statistics object');
+ok($obj->create_spreadsheet,'Create the CSV file');
+ok(-e 'verbose_stats.csv', 'CSV file exists');
+compare_ok('verbose_stats.csv','t/data/expected_group_statitics_verbose.csv', 'Verbose spreadsheet content as expected');
+
+unlink('verbose_stats.csv');
+
+done_testing();