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#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
use Test::Files;
use File::Which;
BEGIN { unshift( @INC, './lib' ) }
BEGIN {
use Test::Most;
use_ok('Bio::Roary::QC::Report');
}
my $kraken_data = [
[ 'assembly1', 'Clostridium', 'Clostridium difficile' ],
[ 'assembly2', 'Escherichia', 'Escherichia coli' ],
[ 'assembly3', 'Streptococcus', 'Streptococcus pneumoniae' ]
];
ok(
my $qc_report_obj = Bio::Roary::QC::Report->new(
input_files => [],
outfile => "kraken_report.csv",
_kraken_data => $kraken_data,
kraken_db => 't/data/kraken_test/',
job_runner => "Local"
),
'QC report object created with no input gff files'
);
ok( $qc_report_obj->report, 'report generated' );
ok( -e 'kraken_report.csv', 'report file exists' );
compare_ok('kraken_report.csv',"t/data/exp_qc_report.csv", 'report file correct' );
unlink('kraken_report.csv');
ok(
$qc_report_obj = Bio::Roary::QC::Report->new(
input_files => [ 't/data/query_1.gff', 't/data/query_2.gff' ],
outfile => "kraken_report.csv",
job_runner => "Local",
kraken_db => 't/data/kraken_test/',
verbose => 0,
),
'QC report object created with data'
);
is( $qc_report_obj->_tmp_directory . '/abc.fna', $qc_report_obj->_nuc_fasta_filename('abc.gff'), 'filename of nuc from gff' );
is(
'sed -n \'/##FASTA/,//p\' abc.gff | grep -v \'##FASTA\' > ' . $qc_report_obj->_tmp_directory . '/abc.fna',
$qc_report_obj->_extract_nuc_fasta_cmd('abc.gff'),
'extract nuc command'
);
ok( my $nuc_files = $qc_report_obj->_extract_nuc_files_from_all_gffs(), 'extract nuc files from gffs' );
is_deeply( [ $qc_report_obj->_tmp_directory . '/query_1.fna', $qc_report_obj->_tmp_directory . '/query_2.fna' ],
$nuc_files, 'check extracted nuc files from gffs list' );
compare_ok( $qc_report_obj->_tmp_directory . '/query_1.fna' ,
't/data/expected_query_1.fna',
'Check FASTA file 1 extracted as expected'
);
compare_ok( $qc_report_obj->_tmp_directory . '/query_2.fna' ,
't/data/expected_query_2.fna',
'Check FASTA file 2 extracted as expected'
);
SKIP:
{
skip "kraken not installed", 2 unless ( which('kraken') );
skip "kraken-report not installed", 2 unless ( which('kraken-report') );
ok( my $kraken_files = $qc_report_obj->_run_kraken_on_nuc_files($nuc_files), 'run kraken over everything' );
is_deeply( [ $qc_report_obj->_tmp_directory . '/query_1.kraken', $qc_report_obj->_tmp_directory . '/query_2.kraken' ],
$kraken_files, 'check kraken files are created from nuc files' );
ok(my $kraken_report_files = $qc_report_obj->_run_kraken_report_on_kraken_files( $kraken_files ), 'build reports');
is_deeply( [ $qc_report_obj->_tmp_directory . '/query_1.kraken.report', $qc_report_obj->_tmp_directory . '/query_2.kraken.report' ],
$kraken_report_files, 'check kraken report files are created from kraken files' );
is_deeply([['query_1','Staphylococcus', 'Staphylococcus aureus'],['query_2','Staphylococcus', 'Staphylococcus aureus']],$qc_report_obj->_parse_kraken_reports($kraken_report_files),'check output report');
ok( $qc_report_obj->report, 'report generated with real data' );
ok( -e 'kraken_report.csv', 'report file exists with real data' );
compare_ok('kraken_report.csv',"t/data/exp_qc_report_real.csv", 'report file correct' );
unlink('kraken_report.csv');
}
done_testing();
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