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#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
use Moose;
use Test::Files;
use File::Slurper qw(read_lines);
BEGIN { unshift( @INC, './t/lib' ) }
with 'TestHelper';
BEGIN { unshift( @INC, './lib' ) }
$ENV{PATH} .= ":./bin";
BEGIN {
use Test::Most;
use_ok('Bio::Roary::AnnotateGroups');
}
my $obj;
ok(
$obj = Bio::Roary::AnnotateGroups->new(
gff_files => [ 't/data/query_1.gff', 't/data/query_2.gff', 't/data/query_3.gff' ],
groups_filename => 't/data/query_groups',
),
'initalise'
);
ok( $obj->reannotate, 'reannotate' );
is_deeply(
$obj->_ids_to_gene_size,
{
'abc_00012' => 188,
'2_3' => 1001,
'1_1' => 959,
'abc_00004' => 716,
'3_3' => 1001,
'3_2' => 725,
'2_2' => 725,
'abc_00006' => 725,
'abc_00008' => 935,
'1_6' => 134,
'abc_00015' => 134,
'3_1' => 959,
'abc_00014' => 134,
'abc_01705' => 1556,
'abc_00013' => 75,
'abc_00010' => 227,
'1_2' => 725,
'abc_00011' => 947,
'abc_00016' => 686,
'2_7' => 134,
'1_3' => 1001,
'2_1' => 959,
'3_5' => 686,
'abc_00002' => 146,
'abc_00003' => 197
},
'gene lengths as expected'
);
is_deeply(
$obj->group_nucleotide_lengths,
{
'group_3' => {
'average' => 1001,
'min' => 1001,
'max' => 1001
},
'group_5' => {
'average' => 686,
'min' => 686,
'max' => 686
},
'group_7' => {
'average' => 134,
'min' => 134,
'max' => 134
},
'group_1' => {
'average' => 959,
'min' => 959,
'max' => 959
},
'group_6' => {
'average' => 134,
'min' => 134,
'max' => 134
},
'group_2' => {
'average' => 725,
'min' => 725,
'max' => 725
}
},
'group lengths'
);
compare_files( 'reannotated_groups_file', 't/data/expected_reannotated_groups_file', 'groups reannotated as expected' );
unlink('reannotated_groups_file');
ok(
$obj = Bio::Roary::AnnotateGroups->new(
gff_files => [ 't/data/gene_name_field/annotation_1.gff', 't/data/gene_name_field/annotation_2.gff' ],
groups_filename => 't/data/gene_name_field/groups',
),
'initalise where gene key is replaced by Name'
);
ok( $obj->reannotate, 'reannotate' );
compare_files('reannotated_groups_file',
't/data/gene_name_field/expected_reannotated_groups_file',
'Reannoated groups file has the gene names transferred'
);
unlink('reannotated_groups_file');
done_testing();
|
