def test_rhinoscleromatis(self):
contigs = 'test/sequences/GCF_000163455.1.fna.gz'
with tempfile.TemporaryDirectory() as tmp_dir:
contigs = gunzip_contigs_if_necessary(contigs, tmp_dir)
results = get_chromosome_mlst_results(self.data_dir, contigs, True)
self.assertEqual(results['ST'], 'ST67 (subsp. rhinoscleromatis)')
self.assertEqual(results['Chr_ST'], 'ST67')
def test_ozanae(self):
contigs = 'test/sequences/GCF_900451425.1.fna.gz'
with tempfile.TemporaryDirectory() as tmp_dir:
contigs = gunzip_contigs_if_necessary(contigs, tmp_dir)
results = get_chromosome_mlst_results(self.data_dir, contigs, True)
self.assertEqual(results['ST'], 'ST90 (subsp. ozanae)')
self.assertEqual(results['Chr_ST'], 'ST90')
def test_83(self):
contigs = 'test/sequences/83.fasta.gz'
with tempfile.TemporaryDirectory() as tmp_dir:
contigs = gunzip_contigs_if_necessary(contigs, tmp_dir)
results = get_chromosome_mlst_results(self.data_dir, contigs, True)
self.assertEqual(results['gapA'], '10')
self.assertEqual(results['infB'], '7')
self.assertEqual(results['mdh'], '1')
self.assertEqual(results['pgi'], '1')
self.assertEqual(results['phoE'], '1')
self.assertEqual(results['rpoB'], '1')
self.assertEqual(results['tonB'], '35')
self.assertEqual(results['ST'], 'ST160')
self.assertEqual(results['Chr_ST'], 'ST160')
def test_unknown_ST(self):
"""
This test has exact matches for alleles but in an unknown ST combination
"""
results = get_chromosome_mlst_results(self.data_dir, 'test/sequences/test_mlst_3.fasta', True)
self.assertEqual(results['gapA'], '44')
self.assertEqual(results['infB'], '56')
self.assertEqual(results['mdh'], '34')
self.assertEqual(results['pgi'], '19')
self.assertEqual(results['phoE'], '30')
self.assertEqual(results['rpoB'], '53')
self.assertEqual(results['tonB'], '55')
self.assertEqual(results['ST'], '0')
self.assertEqual(results['Chr_ST'], '0')
def test_chromosome_inexact(self):
"""
This test is is one base off from ST23 (single substitution in mdh_1 of G to A).
"""
results = get_chromosome_mlst_results(self.data_dir, 'test/sequences/test_mlst_2.fasta', True)
self.assertEqual(results['gapA'], '2')
self.assertEqual(results['infB'], '1')
self.assertEqual(results['mdh'], '1*')
self.assertEqual(results['pgi'], '1')
self.assertEqual(results['phoE'], '9')
self.assertEqual(results['rpoB'], '4')
self.assertEqual(results['tonB'], '12')
self.assertEqual(results['ST'], 'ST23-1LV')
self.assertEqual(results['Chr_ST'], 'ST23-1LV')
def test_chromosome_exact(self):
"""
This test is an exact match for ST23.
"""
results = get_chromosome_mlst_results(self.data_dir, 'test/sequences/test_mlst_1.fasta', True)
self.assertEqual(results['gapA'], '2')
self.assertEqual(results['infB'], '1')
self.assertEqual(results['mdh'], '1')
self.assertEqual(results['pgi'], '1')
self.assertEqual(results['phoE'], '9')
self.assertEqual(results['rpoB'], '4')
self.assertEqual(results['tonB'], '12')
self.assertEqual(results['ST'], 'ST23')
self.assertEqual(results['Chr_ST'], 'ST23')
def test_chromosome_random(self):
"""
This test has just random sequence and should give no MLST call.
"""
results = get_chromosome_mlst_results(self.data_dir, 'test/sequences/test_random.fasta', True)
self.assertEqual(results['gapA'], '-')
self.assertEqual(results['infB'], '-')
self.assertEqual(results['mdh'], '-')
self.assertEqual(results['pgi'], '-')
self.assertEqual(results['phoE'], '-')
self.assertEqual(results['rpoB'], '-')
self.assertEqual(results['tonB'], '-')
self.assertEqual(results['ST'], '0')
self.assertEqual(results['Chr_ST'], '0')
def test_chromosome_exact(self):
"""
This test is an exact match for ST23.
"""
results = get_chromosome_mlst_results(self.mlstblast, self.data_folder,
'test/test_mlst_1.fasta')
self.assertEqual(results['gapA'], '2')
self.assertEqual(results['infB'], '1')
self.assertEqual(results['mdh'], '1')
self.assertEqual(results['pgi'], '1')
self.assertEqual(results['phoE'], '9')
self.assertEqual(results['rpoB'], '4')
self.assertEqual(results['tonB'], '12')
self.assertEqual(results['ST'], 'ST23')
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