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#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
use Test::Files;
BEGIN { unshift( @INC, './lib' ) }
BEGIN {
use Test::Most;
use_ok('Bio::Roary::AssemblyStatistics');
}
my $obj;
ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/input_block_spreadsheet.csv' ), 'initialise spreadsheet' );
my @genes = sort keys %{ $obj->_genes_to_rows };
is_deeply(
\@genes,
[
'SBOV29371', 'SBOV38871', 'SBOV43201', 'STY3593', 'STY4162', 'bcsC_1', 'betC_2', 'comM_2',
'dmsA4_1', 'dosC', 'dsbA_3', 'fadH_1', 'fimD_3', 'fliB_2', 'fliF', 'ftsN',
'gatY_1', 'glfT2', 'group_1000', 'group_1001', 'group_1004', 'group_1006', 'group_1009', 'group_220',
'group_277', 'group_281', 'group_283', 'group_284', 'group_288', 'hemD', 'hsrA_2', 'icsA',
'kdpD', 'ligB_1', 'marT_1', 'nepI', 'rffH', 'rpoS', 'selA_1', 'speC_3',
'sptP', 'srgB', 'stp', 'tmcA', 'tub', 'yadA', 'ybbW_1', 'yhaO_2',
'yicJ_1', 'yigZ'
],
'all gene rows available'
);
is_deeply(
$obj->ordered_genes,
[
'dmsA4_1', 'group_1000', 'group_1001', 'SBOV43201', 'dosC', 'stp', 'fliB_2', 'fliF',
'dsbA_3', 'srgB', 'fimD_3', 'betC_2', 'tmcA', 'tub', 'rffH', 'hemD',
'group_1006', 'STY3593', 'group_1004', 'yigZ', 'group_220', 'glfT2', 'kdpD', 'speC_3',
'ybbW_1', 'sptP', 'SBOV29371', 'rpoS', 'fadH_1', 'yhaO_2', 'bcsC_1', 'STY4162',
'yadA', 'ligB_1', 'icsA', 'marT_1', 'selA_1', 'nepI', 'gatY_1', 'SBOV38871',
'group_288', 'hsrA_2', 'group_281', 'group_283', 'group_284', 'yicJ_1', 'ftsN', 'group_277',
'group_1009', 'comM_2'
],
'ordered genes'
);
is_deeply(
$obj->sample_names_to_column_index,
{
'threeblocks' => 18,
'nocontigs' => 17,
'contigwithgaps' => 16,
'oneblock' => 14,
'threeblocksinversion' => 19,
'oneblockrev' => 15
},
'sample names to column index'
);
is_deeply( $obj->_sample_statistics('oneblock'), { num_blocks => 1, largest_block_size => 50 }, 'one block' );
is_deeply( $obj->_sample_statistics('oneblockrev'), { num_blocks => 1, largest_block_size => 50 }, 'one block reversed' );
is_deeply(
$obj->_sample_statistics('contigwithgaps'),
{ num_blocks => 1, largest_block_size => 50 },
'one block where there are gaps everywhere'
);
is_deeply( $obj->_sample_statistics('nocontigs'), { num_blocks => 50, largest_block_size => 1 }, 'no contiguous blocks' );
is_deeply( $obj->_sample_statistics('threeblocks'), { num_blocks => 3, largest_block_size => 21 }, 'three blocks' );
is_deeply(
$obj->_sample_statistics('threeblocksinversion'),
{ num_blocks => 3, largest_block_size => 20 },
'three blocks with an inversion in the middle'
);
is_deeply( $obj->gene_category_count, { core => 50 }, 'Gene category counts' );
# t/data/gene_category_count.csv
ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/gene_category_count.csv' ),
'initialise spreadsheet with variable numbers of genes in samples' );
is_deeply(
$obj->gene_category_count,
{
'core' => 1,
'cloud' => 4,
'soft_core' => 1,
'shell' => 24
},
'Categories as expected'
);
ok($obj->create_summary_output, 'create output file');
compare_ok('summary_statistics.txt', 't/data/expected_summary_statistics.txt', 'summary statistics as expected');
# t/data/gene_category_count.csv
ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/gene_category_count.csv', core_definition => 0.9667 ),
'initialise spreadsheet with core of 96.67%' );
is_deeply(
$obj->gene_category_count,
{
'core' => 1,
'soft_core' => 1,
'cloud' => 4,
'shell' => 24
},
'Categories as expected with cd of 96.67%'
);
# t/data/gene_category_count.csv
ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/gene_category_count.csv', core_definition => 0.9666 ),
'initialise spreadsheet with core of 96.66%' );
is_deeply(
$obj->gene_category_count,
{
'core' => 2,
'cloud' => 4,
'shell' => 24
},
'Categories as expected with cd of 96.66%'
);
unlink('summary_statistics.txt');
done_testing();
|
