diff Roary/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t @ 0:c47a5f61bc9f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,68 @@
+#!/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();