Move Omp results into a separate resistance column

emollier · May 7, 2019 · 4d85733 · 4d85733
1 parent 593c57f
commit 4d85733
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Showing 4 changed files with 22 additions and 19 deletions.
diff --git a/kleborate/resBLAST.py b/kleborate/resBLAST.py
@@ -139,6 +139,9 @@ def read_class_file(res_class_file):
     if 'NA' in bla_classes:
         bla_classes.remove('NA')
 
+    if 'Omp' not in res_classes:
+        res_classes.append('Omp')
+
     return gene_info, res_classes, bla_classes
 
 
@@ -360,9 +363,9 @@ def check_for_omp_gene_truncations(hits_dict, contigs, omp):
         truncations.append('OmpK36-' + ('%.0f' % best_ompk36_cov) + '%')
 
     if truncations:
-        if 'Bla_Carb' not in hits_dict:
-            hits_dict['Bla_Carb'] = []
-        hits_dict['Bla_Carb'] += truncations
+        if 'Omp' not in hits_dict:
+            hits_dict['Omp'] = []
+        hits_dict['Omp'] += truncations
 
 
 def check_for_ompk36_mutations(hits_dict, contigs, omp):
@@ -381,9 +384,9 @@ def check_for_ompk36_mutations(hits_dict, contigs, omp):
                 coverage = 100.0 * float(hit_length) / gene_len
                 if coverage >= 90.0 and hsp_hit_eval <= 0.001 and identity >= 0.9:
                     if gene_id == 'OmpK36GD' and 'GDGDTY' in hsp_qseq:
-                        hits_dict['Bla_Carb'].append('OmpK36GD')
+                        hits_dict['Omp'].append('OmpK36GD')
                     if gene_id == 'OmpK36TD' and 'GDTDTY' in hsp_qseq:
-                        hits_dict['Bla_Carb'].append('OmpK36TD')
+                        hits_dict['Omp'].append('OmpK36TD')
 
 
 def get_strain_name(full_path):

diff --git a/test/test_res_mgrb_pmrb.py b/test/test_res_mgrb_pmrb.py
@@ -65,7 +65,7 @@ def test_mgrb_missing_non_kp_complex(self):
         """
         results = get_resistance_results(self.data_dir, 'test/sequences/test_res_mgrb_pmrb_4.fasta',
                                          self.args, self.res_headers, False)
-        self.assertFalse('MgrB-' in results['Col'])
+        self.assertTrue('MgrB-' not in results['Col'])
 
     def test_pmrb_early_stop_SRR2098701(self):
         results = get_resistance_results(self.data_dir, 'test/sequences/SRR2098701.fasta',

diff --git a/test/test_res_omp.py b/test/test_res_omp.py
@@ -36,43 +36,43 @@ def setUp(self):
     def test_both_genes_intact(self):
         results = get_resistance_results(self.data_dir, 'test/sequences/test_res_omp_1.fasta',
                                          self.args, self.res_headers, True)
-        self.assertEqual(results['Bla_Carb'], '-')
+        self.assertEqual(results['Omp'], '-')
 
     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/sequences/test_res_omp_2.fasta',
                                          self.args, self.res_headers, True)
-        self.assertTrue('OmpK35-' in results['Bla_Carb'])
+        self.assertTrue('OmpK35-' in results['Omp'])
 
     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/sequences/test_res_omp_3.fasta',
                                          self.args, self.res_headers, True)
-        self.assertTrue('OmpK35-' in results['Bla_Carb'])
+        self.assertTrue('OmpK35-' in results['Omp'])
 
     def test_ompk36_missing(self):
         results = get_resistance_results(self.data_dir, 'test/sequences/test_res_omp_4.fasta',
                                          self.args, self.res_headers, True)
-        self.assertTrue('OmpK36-' in results['Bla_Carb'])
+        self.assertTrue('OmpK36-' in results['Omp'])
 
     def test_ompk36gd(self):
         results = get_resistance_results(self.data_dir, 'test/sequences/test_res_omp_5.fasta',
                                          self.args, self.res_headers, True)
-        self.assertTrue('OmpK36GD' in results['Bla_Carb'])
+        self.assertTrue('OmpK36GD' in results['Omp'])
 
     def test_ompk36td(self):
+        results = get_resistance_results(self.data_dir, 'test/sequences/test_res_omp_6.fasta',
+                                         self.args, self.res_headers, True)
+        self.assertTrue('OmpK36TD' in results['Omp'])
+
+    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/sequences/test_res_omp_6.fasta',
                                          self.args, self.res_headers, False)
-        self.assertFalse('OmpK36TD' in results['Bla_Carb'])
-
-    def test_ompk36td_non_kp_complex(self):
-        results = get_resistance_results(self.data_dir, 'test/sequences/test_res_omp_6.fasta',
-                                         self.args, self.res_headers, True)
-        self.assertTrue('OmpK36TD' in results['Bla_Carb'])
+        self.assertTrue('OmpK36TD' not in results['Omp'])
diff --git a/test/test_res_qrdr.py b/test/test_res_qrdr.py
@@ -60,5 +60,5 @@ def test_gyra_and_parc_non_kp_complex(self):
         """
         results = get_resistance_results(self.data_dir, 'test/sequences/test_res_qrdr_4.fasta',
                                          self.args, self.res_headers, False)
-        self.assertFalse('GyrA-83C' in results['Flq'])
-        self.assertFalse('ParC-84D' in results['Flq'])
+        self.assertTrue('GyrA-83C' not in results['Flq'])
+        self.assertTrue('ParC-84D' not in results['Flq'])