--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/t/Bio/Roary/ReformatInputGFFs.t	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,67 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Data::Dumper;
+use File::Path qw(remove_tree);
+use Test::Files;
+
+BEGIN { unshift( @INC, './lib' ) }
+$ENV{PATH} .= ":./bin";
+
+BEGIN {
+    use Test::Most;
+    use_ok('Bio::Roary::ReformatInputGFFs');
+}
+
+
+my $obj;
+remove_tree('fixed_input_files');
+ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/query_1.gff']), 'initialise with one input gff');
+ok($obj->fix_duplicate_gene_ids, 'fix duplicates with one input gff');
+is_deeply($obj->fixed_gff_files, ['t/data/reformat_input_gffs/query_1.gff'] ,'list of gff files with one input gff, nothing should change');
+ok(!( -d 'fixed_input_files'), 'Directory shouldnt exist because there arent any fixed input files');
+
+
+ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/query_1.gff', 't/data/reformat_input_gffs/query_2.gff',]), 'initialise with 2 input gffs');
+ok(!( -d 'fixed_input_files'), 'Directory shouldnt exist before running');
+is_deeply($obj->_get_ids_for_gff_file('t/data/reformat_input_gffs/query_1.gff'),[
+          '1_1',
+          'abc_00002',
+          'abc_00003',
+          'abc_00004',
+          '1_2'
+        ],'extract ids');
+is_deeply($obj->_get_ids_for_gff_file('t/data/reformat_input_gffs/query_2.gff'),[
+          '1_1',
+          'abc_00002',
+          'abc_00003',
+          'abc_00004',
+          '1_2'
+        ],'extract ids');
+ok($obj->fix_duplicate_gene_ids, 'fix duplicates with 2 input gffs');
+ok(( -d 'fixed_input_files'), 'Directory should exist because there is one gff thats fixed');
+is_deeply($obj->fixed_gff_files, ['t/data/reformat_input_gffs/query_1.gff','fixed_input_files/query_2.gff' ] ,'list of gff files one in the fixed directory');
+ok(( -e 'fixed_input_files/query_2.gff'), 'fixed file should exist');
+compare_ok('fixed_input_files/query_2.gff', 't/data/reformat_input_gffs/expected_fixed_query_2.gff',  'fixed file should have expected changes');
+remove_tree('fixed_input_files');
+
+ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/query_1.gff', 't/data/reformat_input_gffs/query_2.gff', 't/data/reformat_input_gffs/query_3.gff']), 'initialise with 3 input gffs, 2 identical duplicates');
+ok(!( -d 'fixed_input_files'), 'Directory shouldnt exist before running');
+ok($obj->fix_duplicate_gene_ids, 'fix duplicates with 3 input gffs');
+ok(( -d 'fixed_input_files'), 'Directory should exist because there are 2 gffs thats fixed');
+is_deeply($obj->fixed_gff_files, ['t/data/reformat_input_gffs/query_1.gff','fixed_input_files/query_2.gff' ] ,'list of gff files 2 in the fixed directory');
+ok(( -e 'fixed_input_files/query_2.gff'), 'fixed file should exist');
+ok(!( -e 'fixed_input_files/query_3.gff'), 'fixed file should exist');
+compare_ok('fixed_input_files/query_2.gff','t/data/reformat_input_gffs/expected_fixed_query_2.gff',  'fixed file should have expected changes');
+remove_tree('fixed_input_files');
+	
+
+ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/real_1.gff']), 'initialise with 1 gff that has shown to have a bug');
+ok(my $fixed_file = $obj->_add_suffix_to_gene_ids_and_return_new_file('t/data/reformat_input_gffs/real_1.gff', 'id__'), 'fix duplicates');
+ok(( -e 'fixed_input_files/real_1.gff'), 'fixed file should exist');
+compare_ok('fixed_input_files/real_1.gff', 't/data/reformat_input_gffs/expected_real_1.gff',  'fixed file should have expected changes');
+remove_tree('fixed_input_files');
+
+
+done_testing();
+