--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/t/Bio/Roary/AnnotateGroups.t	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,119 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Data::Dumper;
+use Moose;
+use Test::Files;
+use File::Slurper qw(read_lines);
+BEGIN { unshift( @INC, './t/lib' ) }
+with 'TestHelper';
+
+BEGIN { unshift( @INC, './lib' ) }
+$ENV{PATH} .= ":./bin";
+
+BEGIN {
+    use Test::Most;
+    use_ok('Bio::Roary::AnnotateGroups');
+}
+
+my $obj;
+
+ok(
+    $obj = 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',
+    ),
+    'initalise'
+);
+
+ok( $obj->reannotate, 'reannotate' );
+is_deeply(
+    $obj->_ids_to_gene_size,
+    {
+        'abc_00012' => 188,
+        '2_3'       => 1001,
+        '1_1'       => 959,
+        'abc_00004' => 716,
+        '3_3'       => 1001,
+        '3_2'       => 725,
+        '2_2'       => 725,
+        'abc_00006' => 725,
+        'abc_00008' => 935,
+        '1_6'       => 134,
+        'abc_00015' => 134,
+        '3_1'       => 959,
+        'abc_00014' => 134,
+        'abc_01705' => 1556,
+        'abc_00013' => 75,
+        'abc_00010' => 227,
+        '1_2'       => 725,
+        'abc_00011' => 947,
+        'abc_00016' => 686,
+        '2_7'       => 134,
+        '1_3'       => 1001,
+        '2_1'       => 959,
+        '3_5'       => 686,
+        'abc_00002' => 146,
+        'abc_00003' => 197
+    },
+    'gene lengths as expected'
+);
+
+is_deeply(
+    $obj->group_nucleotide_lengths,
+    {
+        'group_3' => {
+            'average' => 1001,
+            'min'     => 1001,
+            'max'     => 1001
+        },
+        'group_5' => {
+            'average' => 686,
+            'min'     => 686,
+            'max'     => 686
+        },
+        'group_7' => {
+            'average' => 134,
+            'min'     => 134,
+            'max'     => 134
+        },
+        'group_1' => {
+            'average' => 959,
+            'min'     => 959,
+            'max'     => 959
+        },
+        'group_6' => {
+            'average' => 134,
+            'min'     => 134,
+            'max'     => 134
+        },
+        'group_2' => {
+            'average' => 725,
+            'min'     => 725,
+            'max'     => 725
+        }
+    },
+    'group lengths'
+);
+
+compare_files( 'reannotated_groups_file', 't/data/expected_reannotated_groups_file', 'groups reannotated as expected' );
+
+unlink('reannotated_groups_file');
+
+
+ok(
+    $obj = Bio::Roary::AnnotateGroups->new(
+        gff_files       => [ 't/data/gene_name_field/annotation_1.gff', 't/data/gene_name_field/annotation_2.gff' ],
+        groups_filename => 't/data/gene_name_field/groups',
+    ),
+    'initalise where gene key is replaced by Name'
+);
+ok( $obj->reannotate, 'reannotate' );
+compare_files('reannotated_groups_file',
+    't/data/gene_name_field/expected_reannotated_groups_file',
+    'Reannoated groups file has the gene names transferred'
+);
+unlink('reannotated_groups_file');
+
+done_testing();
+