Fixing tests

staramr/blast/results/pointfinder/BlastResultsParserPointfinder.py

@@ -48,7 +48,8 @@ def __init__(self, file_blast_map, blast_database, pid_threshold, plength_thresh
 
     def _create_hit(self, file, database_name, blast_record):
         logger.debug("database_name=%s", database_name)
-        if (database_name == '16S_rrsD') or (database_name == '23S'):
+        if (database_name.startswith('16S_rrs') or database_name.startswith('16S-rrs') \
+            or (database_name == '23S')):
             return PointfinderHitHSPRNA(file, blast_record)
         elif ('promoter' in database_name):
             return PointfinderHitHSPPromoter(file, blast_record, database_name)            

staramr/blast/results/pointfinder/nucleotide/PointfinderHitHSPRNA.py

@@ -25,7 +25,7 @@ def get_amr_gene_name(self):
         # pointfinder/campylobacter/23S.fsa -> 23S_1_LR134511.1
         # pointfinder/neisseria_gonorrhoeae/23S-rRNA-a1.fsa -> 23S-rRNA-a1_1_AE004969.1
         if name.startswith("16S_rrs"): name = name.split("_")[0] + "_" + name.split("_")[1]
-        elif name.startswith("16S"): name = "16S"
+        elif name.startswith("16S-rrs"): name = name.split("_")[0].replace("-", "_", 1) # Ex: 16S-rrsD_1_CP049983.1
         elif name.startswith("23S"): name = "23S"
         else: name = name.split("_")[0]
 

staramr/tests/integration/detection/test_AMRDetection.py

@@ -532,7 +532,7 @@ def testPointfinderSalmonellaA67PSuccessNoPhenotype(self):
         pointfinder_results = amr_detection.get_pointfinder_results()
         self.assertEqual(len(pointfinder_results.index), 1, 'Wrong number of rows in result')
 
-        result = pointfinder_results[pointfinder_results['Gene'] == 'gyrA (A67P)']
+        result = pointfinder_results[pointfinder_results['Gene'] == 'gyrA_1_MH933946.1 (A67P)']
         self.assertEqual(len(result.index), 1, 'Wrong number of results detected')
         self.assertEqual(result.index[0], 'gyrA-A67P', msg='Wrong file')
         self.assertEqual(result['Type'].iloc[0], 'codon', msg='Wrong type')
@@ -549,7 +549,7 @@ def testPointfinderSalmonellaA67PSuccessNoPhenotype(self):
         self.assertEqual(len(records), 1, 'Wrong number of hit records')
 
         expected_records = SeqIO.to_dict(SeqIO.parse(file, 'fasta'))
-        self.assertEqual(expected_records['gyrA'].seq.upper(), records['gyrA'].seq.upper(), "records don't match")
+        self.assertEqual(expected_records['gyrA'].seq.upper(), records['gyrA_1_MH933946.1'].seq.upper(), "records don't match")
 
     def testPointfinderSalmonellaA67PDelEndSuccess(self):
         pointfinder_database = PointfinderBlastDatabase(self.pointfinder_dir, 'salmonella')
@@ -729,7 +729,7 @@ def testPointfinderSalmonella_16S_rrSD_C1065T_Success(self):
         self.assertEqual(len(records), 1, 'Wrong number of hit records')
 
         expected_records = SeqIO.to_dict(SeqIO.parse(file, 'fasta'))
-        self.assertEqual(expected_records['16S_rrsD'].seq.upper(), records['16S_rrsD'].seq.upper(),
+        self.assertEqual(expected_records['16S_rrsD'].seq.upper(), records['16S-rrsD_1_CP049983.1'].seq.upper(),
                          "records don't match")
 
 
@@ -1016,9 +1016,9 @@ def testResfinderPointfinderSalmonella_16S_C1065T_gyrA_A67_beta_lactam_Success(s
         records = SeqIO.to_dict(SeqIO.parse(hit_file, 'fasta'))
         self.assertEqual(len(records), 2, 'Wrong number of hit records')
         expected_records1 = SeqIO.to_dict(SeqIO.parse(path.join(self.test_data_dir, 'gyrA-A67P.fsa'), 'fasta'))
-        self.assertEqual(expected_records1['gyrA'].seq.upper(), records['gyrA'].seq.upper(), "records don't match")
+        self.assertEqual(expected_records1['gyrA'].seq.upper(), records['gyrA_1_MH933946.1'].seq.upper(), "records don't match")
         expected_records2 = SeqIO.to_dict(SeqIO.parse(path.join(self.test_data_dir, '16S_rrsD-1T1065.fsa'), 'fasta'))
-        self.assertEqual(expected_records2['16S_rrsD'].seq.upper(), records['16S_rrsD'].seq.upper(),
+        self.assertEqual(expected_records2['16S_rrsD'].seq.upper(), records['16S-rrsD_1_CP049983.1'].seq.upper(),
                          "records don't match")
 
     def testResfinderPointfinderSalmonellaExcludeGenesListSuccess(self):
@@ -1028,7 +1028,7 @@ def testResfinderPointfinderSalmonellaExcludeGenesListSuccess(self):
         amr_detection = AMRDetectionResistance(self.resfinder_database, self.resfinder_drug_table,
                                                self.cge_drug_table, blast_handler,
                                                self.pointfinder_drug_table, pointfinder_database,
-                                               output_dir=self.outdir.name, genes_to_exclude=['gyrA'])
+                                               output_dir=self.outdir.name, genes_to_exclude=['gyrA_1_MH933946.1'])
 
         file = path.join(self.test_data_dir, "16S_gyrA_beta-lactam.fsa")
         files = [file]
@@ -1115,9 +1115,9 @@ def testResfinderPointfinderSalmonella_16Src_C1065T_gyrArc_A67_beta_lactam_Succe
         records = SeqIO.to_dict(SeqIO.parse(hit_file, 'fasta'))
         self.assertEqual(len(records), 2, 'Wrong number of hit records')
         expected_records1 = SeqIO.to_dict(SeqIO.parse(path.join(self.test_data_dir, 'gyrA-A67P.fsa'), 'fasta'))
-        self.assertEqual(expected_records1['gyrA'].seq.upper(), records['gyrA'].seq.upper(), "records don't match")
+        self.assertEqual(expected_records1['gyrA'].seq.upper(), records['gyrA_1_MH933946.1'].seq.upper(), "records don't match")
         expected_records2 = SeqIO.to_dict(SeqIO.parse(path.join(self.test_data_dir, '16S_rrsD-1T1065.fsa'), 'fasta'))
-        self.assertEqual(expected_records2['16S_rrsD'].seq.upper(), records['16S_rrsD'].seq.upper(),
+        self.assertEqual(expected_records2['16S_rrsD'].seq.upper(), records['16S-rrsD_1_CP049983.1'].seq.upper(),
                          "records don't match")
 
     def testResfinderExcludeNonMatches(self):