def test_iro_incomplete(self):
"""
This test is an exact match for only one allele.
"""
results = get_iro_mlst_results(self.mlstblast, self.data_folder,
'test/test_iro_4.fasta')
self.assertEqual(results['iroB'], '-')
self.assertEqual(results['iroC'], '1')
self.assertEqual(results['iroD'], '-')
self.assertEqual(results['iroN'], '-')
self.assertEqual(results['Salmochelin'], '-')
self.assertEqual(results['SmST'], '0')
def test_iro_novel(self):
"""
This test is an exact match for alleles, but an unknown combination.
"""
results = get_iro_mlst_results(self.mlstblast, self.data_folder,
'test/test_iro_3.fasta')
self.assertEqual(results['iroB'], '11')
self.assertEqual(results['iroC'], '1')
self.assertEqual(results['iroD'], '18')
self.assertEqual(results['iroN'], '5')
self.assertEqual(results['Salmochelin'], 'iro unknown')
self.assertEqual(results['SmST'], '0')
def test_iro_exact(self):
"""
This test is an exact match for SmST33.
"""
results = get_iro_mlst_results(self.mlstblast, self.data_folder,
'test/test_iro_1.fasta')
self.assertEqual(results['iroB'], '22')
self.assertEqual(results['iroC'], '33')
self.assertEqual(results['iroD'], '12')
self.assertEqual(results['iroN'], '15')
self.assertEqual(results['Salmochelin'], 'iro 2')
self.assertEqual(results['SmST'], '33')
def test_iro_random(self):
"""
This test has just random sequence and should give no iro call.
"""
results = get_iro_mlst_results(self.mlstblast, self.data_folder,
'test/test_random.fasta')
self.assertEqual(results['iroB'], '-')
self.assertEqual(results['iroC'], '-')
self.assertEqual(results['iroD'], '-')
self.assertEqual(results['iroN'], '-')
self.assertEqual(results['Salmochelin'], '-')
self.assertEqual(results['SmST'], '0')
def test_iro_inexact(self):
"""
This test is an inexact match for SmST33. There are single base changes in iroC and in
iroN.
"""
results = get_iro_mlst_results(self.mlstblast, self.data_folder,
'test/test_iro_2.fasta')
self.assertEqual(results['iroB'], '22')
self.assertEqual(results['iroC'], '33*')
self.assertEqual(results['iroD'], '12')
self.assertEqual(results['iroN'], '15*')
self.assertEqual(results['Salmochelin'], 'iro 2')
self.assertEqual(results['SmST'], '33-2LV')
def get_all_results(self, contigs):
results = {'strain': get_strain_name(contigs)}
results.update(get_contig_stat_results(contigs))
results.update(get_species_results(contigs, self.data_dir))
kp_complex = is_kp_complex(results)
results.update(
get_chromosome_mlst_results(self.data_dir, contigs, kp_complex))
results.update(get_ybt_mlst_results(self.data_dir, contigs))
results.update(get_clb_mlst_results(self.data_dir, contigs))
results.update(get_iuc_mlst_results(self.data_dir, contigs))
results.update(get_iro_mlst_results(self.data_dir, contigs))
results.update(get_hypermucoidy_results(self.data_dir, contigs))
results.update(get_wzi_and_k_locus_results(self.data_dir, contigs))
results.update(
get_resistance_results(self.data_dir, contigs, self.args,
self.res_headers, kp_complex))
results.update(get_summary_results(results, self.res_headers))
return results