def test_res_counts_2(self):
self.results['AGly_acquired'] = 'a'
self.results['Flq_acquired'] = 'b;c'
self.results['Tet_acquired'] = 'd;e;f'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '6')
def test_res_score_7(self):
self.results['Bla_chr'] = 'a'
self.results['Bla_ESBL_acquired'] = 'b'
self.results['Bla_Carb_acquired'] = 'c'
self.results['Col_mutations'] = 'd'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '3')
def test_res_counts_5(self):
"""
Bla genes in columns other than 'Bla_chr' (e.g. 'Bla_acquired') should add to the counts.
"""
self.results['Tet_acquired'] = 'a;b;c'
self.results['Bla_acquired'] = 'd'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '2')
self.assertEqual(summary_results['num_resistance_genes'], '4')
def test_res_counts_6(self):
"""
Omp gene truncations should not add to the gene or class counts.
"""
self.results['AGly_acquired'] = 'a'
self.results['Flq_acquired'] = 'b;c'
self.results['Tet_acquired'] = 'd;e;f'
self.results['Omp_mutations'] = 'g;h'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '6')
def test_res_counts_11(self):
"""
Spurious hits should not add to either the gene or class counts.
"""
self.results['AGly_acquired'] = 'a'
self.results['Flq_acquired'] = 'b'
self.results['Tet_acquired'] = 'c'
self.results['spurious_resistance_hits'] = 'd;e;f'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '3')
def test_res_counts_9(self):
"""
Mutations should add to the class count but not to the gene count (because that is for
acquired resistance genes).
"""
self.results['AGly_acquired'] = 'a'
self.results['Tet_acquired'] = 'b;c'
self.results['Col_mutations'] = 'd'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '3')
def test_res_counts_3(self):
"""
Intrinsic Bla genes should not add to the counts.
"""
self.results['AGly_acquired'] = 'a'
self.results['Flq_acquired'] = 'b;c'
self.results['Tet_acquired'] = 'd;e;f'
self.results['Bla_acquired'] = 'g'
self.results['Bla_chr'] = 'h'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '4')
self.assertEqual(summary_results['num_resistance_genes'], '7')
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_nothing(self):
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '0')
self.assertEqual(summary_results['resistance_score'], '0')
self.assertEqual(summary_results['num_resistance_classes'], '0')
self.assertEqual(summary_results['num_resistance_genes'], '0')
def test_vir_score_7(self):
self.results['Aerobactin'] = 'a'
self.results['Colibactin'] = 'b'
self.results['Yersiniabactin'] = 'c'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '5')
def test_vir_score_4(self):
self.results['Aerobactin'] = 'a'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '3')
def test_res_score_8(self):
self.results['Col_acquired'] = 'a'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '0')
def test_res_score_4(self):
self.results['Bla_chr'] = 'a'
self.results['Bla_Carb_acquired'] = 'b'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '2')
def test_res_score_1(self):
self.results['Bla_chr'] = 'a'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '0')
