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|
#!/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::ContigsToGeneIDsFromGFF');
}
ok(
my $obj = Bio::Roary::ContigsToGeneIDsFromGFF->new(
gff_file => 't/data/query_1.gff'
),
'Initialise contigs to gene ids obj'
);
is_deeply(
$obj->contig_to_ids,
{
'abc|SC|contig000001' => [
'1_1', 'abc_00002', 'abc_00003', 'abc_00004', '1_2', 'abc_00006', '1_3', 'abc_00008',
'abc_00010', 'abc_00011', 'abc_00012', 'abc_00014', '1_6', 'abc_00016'
]
},
'Contigs match expected with standard output'
);
ok(
$obj = Bio::Roary::ContigsToGeneIDsFromGFF->new(
gff_file => 't/data/query_1_alternative_patterns.gff'
),
'Initialise contigs to gene ids obj with alternative ID patterns'
);
is_deeply(
$obj->contig_to_ids,
{
'abc|SC|contig000001' => [ '1_1', 'abc_00002', 'abc_00003', 'abc_00004', '1_2', 'abc_00006' ]
},
'Contigs match expected with alternative output'
);
is_deeply(
$obj->_genes_annotation,
[
{
'database_annotation_exists' => 1,
'product' => 'superantigen-like protein',
'end' => '3337',
'start' => '2621',
'contig' => 'abc|SC|contig000001',
'id_name' => 'abc_00004'
},
{
'database_annotation_exists' => 1,
'product' => 'hypothetical protein',
'end' => '4170',
'start' => '3445',
'contig' => 'abc|SC|contig000001',
'id_name' => '1_2'
},
{
'database_annotation_exists' => 1,
'product' => 'superantigen-like protein',
'end' => '4990',
'start' => '4265',
'contig' => 'abc|SC|contig000001',
'id_name' => 'abc_00006'
}
],
'Product annotation with non standard format'
);
done_testing();
|
