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|
#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
BEGIN { unshift( @INC, './lib' ) }
BEGIN {
use Test::Most;
use_ok('Bio::Roary::AccessoryClustering');
}
my $identity_to_num_clusters = {
'1' => [ 10, 10 ],
'0.99' => [ 4, 5 ],
'0.95' => [ 2, 4 ],
'0.90' => [ 1, 1 ],
};
for my $percentage_identity ( keys %{$identity_to_num_clusters} ) {
ok(
my $obj = Bio::Roary::AccessoryClustering->new(
input_file => 't/data/input_accessory_binary.fa',
identity => $percentage_identity
),
"initialise object with identity of $percentage_identity"
);
ok( my @clusters = keys %{ $obj->clusters_to_samples }, "build the clusters for $percentage_identity" );
ok( $obj->sample_weights, "build samples weights for $percentage_identity" );
ok( $obj->samples_to_clusters, "build samples to clusters for $percentage_identity" );
my $min_cluster_size = $identity_to_num_clusters->{$percentage_identity}->[0];
my $max_cluster_size = $identity_to_num_clusters->{$percentage_identity}->[1];
ok(
( @clusters >= $min_cluster_size && @clusters <= $max_cluster_size ? 1 : 0 ),
"check number of clusters as expected, allowing for some variation for $percentage_identity"
);
}
my $obj = Bio::Roary::AccessoryClustering->new(
input_file => 't/data/input_accessory_binary.fa',
identity => 0.9
);
is_deeply(
$obj->samples_to_clusters,
{
'seq6' => 'seq1',
'seq3' => 'seq1',
'seq7' => 'seq1',
'seq9' => 'seq1',
'seq10' => 'seq1',
'seq2' => 'seq1',
'seq8' => 'seq1',
'seq1' => 'seq1',
'seq4' => 'seq1',
'seq5' => 'seq1'
},
'samples to clusters'
);
my @sample_weights = values %{ $obj->sample_weights };
is_deeply( \@sample_weights, [ 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1 ], 'sample weights' );
$obj = Bio::Roary::AccessoryClustering->new(
input_file => 't/data/input_accessory_binary.fa',
identity => 1
);
is_deeply(
$obj->samples_to_clusters,
{
'seq6' => 'seq6',
'seq3' => 'seq3',
'seq7' => 'seq7',
'seq9' => 'seq9',
'seq10' => 'seq10',
'seq2' => 'seq2',
'seq8' => 'seq8',
'seq1' => 'seq1',
'seq4' => 'seq4',
'seq5' => 'seq5'
},
'samples to clusters'
);
@sample_weights = values %{ $obj->sample_weights };
is_deeply( \@sample_weights, [ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ], 'sample weights' );
$obj = Bio::Roary::AccessoryClustering->new(
input_file => 't/data/large_accessory_binary_genes.fa'
);
ok( my @clusters = keys %{ $obj->clusters_to_samples }, "build the clusters for large_accessory_binary_genes.fa" );
ok( $obj->sample_weights, "build samples weights for large_accessory_binary_genes.fa" );
ok( $obj->samples_to_clusters, "build samples to clusters for large_accessory_binary_genes.fa" );
ok(
( @clusters >= 6 && @clusters <= 14 ? 1 : 0 ),
"check number of clusters as expected, allowing for some variation for large_accessory_binary_genes.fa"
);
unlink('_accessory_clusters');
unlink('_accessory_clusters.clstr');
done_testing();
|
