def test_res_07(self):
results = get_resistance_results(self.data_dir,
'test/test_res_alleles/07.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['Tet_acquired'], '-')
self.assertEqual(results['Bla_acquired'], 'ABC-2*')
self.assertEqual(results['Bla_ESBL_acquired'], '-')
self.assertEqual(results['spurious_resistance_hits'], '-')
def test_ompk35_frameshift(self):
"""
A frameshift in OmpK35 should cause an early stop and lead to a carbapenem resistance call.
"""
results = get_resistance_results(
self.data_dir, 'test/test_res_omp/test_res_omp_2.fasta', self.args,
self.res_headers, True)
self.assertTrue('OmpK35-' in results['Omp_mutations'])
def test_ompk36td_non_kp_complex(self):
"""
Setting the Kp complex variable to False should turn off the OmpK tests.
"""
results = get_resistance_results(
self.data_dir, 'test/test_res_omp/test_res_omp_6.fasta', self.args,
self.res_headers, False)
self.assertTrue('OmpK36TD' not in results['Omp_mutations'])
def test_ompk35_early_stop(self):
"""
This tests an early stop mutation (without a frameshift) in OmpK35.
"""
results = get_resistance_results(
self.data_dir, 'test/test_res_omp/test_res_omp_3.fasta', self.args,
self.res_headers, True)
self.assertTrue('OmpK35-' in results['Omp_mutations'])
def test_res_05(self):
"""
Same as test_res_04, but with the hit on the other strand.
"""
results = get_resistance_results(self.data_dir,
'test/test_res_aac/05.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['AGly_acquired'], 'Aac6Ib-cr^')
def test_gyra_and_parc_non_kp_complex(self):
"""
Setting the Kp complex variable to False should turn off the QRDR tests.
"""
results = get_resistance_results(
self.data_dir, 'test/test_res_qrdr/test_res_qrdr_4.fasta',
self.args, self.res_headers, False)
self.assertTrue('GyrA-83C' not in results['Flq_mutations'])
self.assertTrue('ParC-84D' not in results['Flq_mutations'])
def test_mgrb_missing_non_kp_complex(self):
"""
Setting the Kp complex variable to False should turn off the MgrB/PmrB tests.
"""
results = get_resistance_results(
self.data_dir,
'test/test_res_mgrb_pmrb/test_res_mgrb_pmrb_4.fasta', self.args,
self.res_headers, False)
self.assertTrue('MgrB-' not in results['Col_mutations'])
def test_shv_06(self):
"""
This test has SHV-29 plus an inhibition mutation.
"""
results = get_resistance_results(self.data_dir,
'test/test_shv/06.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Bla_ESBL_inhR_acquired'], 'SHV-29* +234Y')
self.assertEqual(results['SHV_mutations'], '234Y;238A;35Q')
def test_shv_05(self):
"""
This test has an exact match for SHV-29.
"""
results = get_resistance_results(self.data_dir,
'test/test_shv/05.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-29')
self.assertEqual(results['SHV_mutations'], '238A;35Q')
def test_pmrb_frameshift(self):
"""
A frameshift in pmrB should cause an early stop and lead to a colisitin resistance call.
"""
results = get_resistance_results(
self.data_dir,
'test/test_res_mgrb_pmrb/test_res_mgrb_pmrb_2.fasta', self.args,
self.res_headers, True)
self.assertTrue('PmrB-' in results['Col_mutations'])
def test_pmrb_early_stop(self):
"""
This tests an early stop mutation (without a frameshift) in pmrB.
"""
results = get_resistance_results(
self.data_dir,
'test/test_res_mgrb_pmrb/test_res_mgrb_pmrb_3.fasta', self.args,
self.res_headers, True)
self.assertTrue('PmrB-' in results['Col_mutations'])
def test_shv_03(self):
"""
Same as test 2, but the gene is on the reverse strand.
"""
results = get_resistance_results(self.data_dir,
'test/test_shv/03.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-1* +238Y')
self.assertEqual(results['SHV_mutations'], '238Y')
def test_shv_01(self):
"""
This test has an exact match for SHV-1.
"""
results = get_resistance_results(self.data_dir,
'test/test_shv/01.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Bla_chr'], 'SHV-1')
self.assertEqual(results['SHV_mutations'], '-')
def test_shv_08(self):
"""
This test has SHV-1 with a synonymous mutation in the omega loop (so not reported).
"""
results = get_resistance_results(self.data_dir,
'test/test_shv/08.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Bla_chr'], 'SHV-1^')
self.assertEqual(results['SHV_mutations'], '-')
def test_res_04(self):
"""
This is a tricky one (and the one which first highlighted the problem). The best bit-score
match is for a partial hit to Ant3''Ih-Aac6-IId, but the correct answer is Aac6Ib-cr, which
has a full coverage hit.
"""
results = get_resistance_results(self.data_dir,
'test/test_res_aac/04.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['AGly_acquired'], 'Aac6Ib-cr^')
def test_shv_04(self):
"""
This test has a match for SHV-1 with a mutation at site 50 (G -> Y). This doesn't change
resistance and so won't be reported.
"""
results = get_resistance_results(self.data_dir,
'test/test_shv/04.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Bla_chr'], 'SHV-1*')
self.assertEqual(results['SHV_mutations'], '-')
def test_shv_09(self):
"""
This test has SHV-1 with a nonsynonymous mutation in the omega loop (so it is reported).
"""
results = get_resistance_results(self.data_dir,
'test/test_shv/09.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-1* +174R')
self.assertEqual(results['SHV_mutations'],
'174R;omega-loop=RWETELNEALRGDARD')
def test_shv_07(self):
"""
This test has SHV-1 with position 238 deleted. Since it's not in the omega loop, this isn't
reported and doesn't have an effect.
"""
results = get_resistance_results(self.data_dir,
'test/test_shv/07.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Bla_chr'], 'SHV-1*')
self.assertEqual(results['SHV_mutations'], '-')
def test_res_09(self):
results = get_resistance_results(self.data_dir,
'test/test_res_alleles/09.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['Tet_acquired'], '-')
self.assertTrue(results['Bla_acquired'] == 'ABC-1^'
or results['Bla_acquired'] == 'ABC-2^')
self.assertTrue(results['Bla_ESBL_acquired'] == 'ABC-3^'
or results['Bla_ESBL_acquired'] == 'ABC-4^')
self.assertEqual(results['spurious_resistance_hits'], '-')
def test_shv_02(self):
"""
This test has a match for SHV-1 with a mutation at site 238 (G -> Y). This changes the
class to ESBL, so the mutation is included in the
"""
results = get_resistance_results(self.data_dir,
'test/test_shv/02.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-1* +238Y')
self.assertEqual(results['SHV_mutations'], '238Y')
def test_res_11(self):
"""
This test has the ABC-1 gene but with a stop codon in the middle.
"""
results = get_resistance_results(self.data_dir,
'test/test_res_alleles/11.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['Tet_acquired'], '-')
self.assertEqual(results['Bla_acquired'], '-')
self.assertEqual(results['Bla_ESBL_acquired'], '-')
self.assertEqual(results['truncated_resistance_hits'], 'ABC-1*-50%')
def test_res_12(self):
"""
This test has the ABC-1 gene but missing the first (start) codon.
"""
results = get_resistance_results(self.data_dir,
'test/test_res_alleles/12.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['Tet_acquired'], '-')
self.assertEqual(results['Bla_acquired'], '-')
self.assertEqual(results['Bla_ESBL_acquired'], '-')
self.assertEqual(results['truncated_resistance_hits'], 'ABC-1?-0%')
def test_res_13(self):
"""
This test has the ABC-1 gene but at only 50% coverage, so it goes to spurious hits.
"""
results = get_resistance_results(self.data_dir,
'test/test_res_alleles/13.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['Tet_acquired'], '-')
self.assertEqual(results['Bla_acquired'], '-')
self.assertEqual(results['Bla_ESBL_acquired'], '-')
self.assertEqual(results['spurious_resistance_hits'], 'ABC-1?-50%')
def get_all_results(self, contigs):
results = {'strain': get_strain_name(contigs)}
results.update(get_species_results(contigs, self.data_dir))
kp_complex = is_kp_complex(results)
results.update(get_contig_stat_results(contigs, is_kp_complex))
results.update(
get_chromosome_mlst_results(self.data_dir, contigs, kp_complex,
self.args))
results.update(get_ybt_mlst_results(self.data_dir, contigs, self.args))
results.update(get_clb_mlst_results(self.data_dir, contigs, self.args))
results.update(get_iuc_mlst_results(self.data_dir, contigs, self.args))
results.update(get_iro_mlst_results(self.data_dir, contigs, self.args))
results.update(get_rmp_mlst_results(self.data_dir, contigs, self.args))
results.update(get_rmpa2_results(self.data_dir, contigs, self.args))
results.update(
get_wzi_and_k_locus_results(self.data_dir, contigs, self.args))
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
def test_tem(self):
results = get_resistance_results(self.data_dir,
'test/test_res_tem/tem.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['Bla_ESBL_acquired'], '-')
self.assertEqual(results['Bla_acquired'], 'TEM-1D^')
def test_gyra_and_parc(self):
results = get_resistance_results(
self.data_dir, 'test/test_res_qrdr/test_res_qrdr_4.fasta',
self.args, self.res_headers, True)
self.assertTrue('GyrA-83C' in results['Flq_mutations'])
self.assertTrue('ParC-84D' in results['Flq_mutations'])
def test_no_mutations(self):
results = get_resistance_results(
self.data_dir, 'test/test_res_qrdr/test_res_qrdr_1.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['Flq_mutations'], '-')
def test_ompk36td(self):
results = get_resistance_results(
self.data_dir, 'test/test_res_omp/test_res_omp_6.fasta', self.args,
self.res_headers, True)
self.assertTrue('OmpK36TD' in results['Omp_mutations'])
def test_res_03(self):
results = get_resistance_results(self.data_dir,
'test/test_res_aac/03.fasta',
self.args, self.res_headers, True)
self.assertEqual(results['AGly_acquired'], 'Aac6-31*')
def test_both_genes_intact(self):
results = get_resistance_results(
self.data_dir, 'test/test_res_omp/test_res_omp_1.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Omp_mutations'], '-')
