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#!/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::ReorderSpreadsheet');
}
ok(
my $obj = Bio::Roary::ReorderSpreadsheet->new(
tree_file => 't/data/reorder_isolates.tre',
spreadsheet => 't/data/reorder_isolates_input.csv',
output_filename => 'reorder_isolates_output.csv',
sortby => 'height'
),
'initialise reordering the spreadsheet'
);
is_deeply($obj->_column_mappings,[0,1,2,3,4,5,6,7,8,9,10,11,12,13],'Column mappings with fixed in same order and end columns ordered by tree file');
ok( $obj->reorder_spreadsheet(), 'run the reorder method' );
ok( -e $obj->output_filename, 'check the output file exists' );
compare_ok('t/data/reorder_isolates_expected_output.csv',
'reorder_isolates_output.csv',
'content of the spreadsheet as expected'
);
unlink('reorder_isolates_output.csv');
done_testing();
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