Mercurial > repos > dereeper > roary_plots
diff Roary/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t @ 0:c47a5f61bc9f draft
Uploaded
author | dereeper |
---|---|
date | Fri, 14 May 2021 20:27:06 +0000 |
parents | |
children |
line wrap: on
line diff
--- /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();