ADD: tests for HamronizationNormalizer

- Updated 'run_argnorm.py' to support the 'hamronization' tool option rather than the '--hamronization' flag
- Removed '@pytest.mark.parametrize('hamronized', [True, False])' in 'test_normalizers.py'. Added test_hamronization_normalizer() which normalizes and tests every file in examples/hamronized
- Updated example outputs in `outputs/` directory to match changes to input_gene and reference_gene processing in HamronizationNormalizer

- Notes on changes to example outputs:
1) `resfinder.resfinder.reads.tsv` and `resfinder.resfinder.orfs.tsv`: ant(6)-Ia, cat, tet(X), and tet(O/32/O) have been mapped to their exact entries in resfinder ARO mapping because their reference_accession is also being used
2) `abricate.resfinder.tsv`: aadA24_1 has been mapped to its exact entry in resfinder ARO mapping. blaCTX-M-63_1_EU660216 and blaCARB-4_1_FJ785525 don't exist in the resfinder database anymore. They were previously mapped as their gene_symbols (blaCTX-M-63 and blaCARB-4) could be mapped to other genes. Now, as their reference_accession is also used, they aren't mapped to AROs anymore.
3) `abricate.ncbi.tsv`: Many new genes have been mapped to the ARO (e.g. dfrB3). However, there has been no change to the preprocessing of ncbi or amrfinderplus inputs. These genes are getting mapped as HamronizationNormalizer combines ARO mapping tables of all dbs, and these genes are being mapped to ARO mapping tables of other dbs. This will be corrected in a future commit where the gene_name of ncbi and amrfinderplus inputs will be used (this will pinpoint the exact unique gene in NCBI ARO mapping).

Author: Vedanth-Ramji

integration_tests/run_argnorm.py

@@ -6,16 +6,16 @@
 os.makedirs('integration_tests/outputs/hamronized', exist_ok=True)
 
 def run_cli_test(tool, file, folder, db=None):
+    if folder == 'hamronized':
+        tool = 'hamronization'
+
     command = [
         'argnorm',
         tool,
         '-i', f'examples/{folder}/{file}',
         '-o', f'integration_tests/outputs/{folder}/{file}'
     ]
 
-    if folder == 'hamronized':
-        command.append('--hamronized')
-
     if tool in  ['abricate', 'groot']:
         command += ['--db', db]
 
@@ -41,6 +41,8 @@ def run_cli_test(tool, file, folder, db=None):
 
 for db in ['ARGANNOT', 'argannot', 'MEGAres', 'megares', 'ncbi', 'resfinder', 'resfinderfg']:
     file  = f'abricate.{db.lower()}.tsv'
-    run_cli_test('abricate', file, 'hamronized', db=db)
+    run_cli_test('hamronization', file, 'hamronized', db=db)
     if not 'resfinder' in db:
         run_cli_test('abricate', file, 'raw', db=db)
+
+run_cli_test('hamronization', 'combined_hamronization.tsv', 'hamronized')

outputs/hamronized/abricate.ncbi.tsv

@@ -528,7 +528,7 @@ GMGC10.008_177_033.ERMX	GMGC10.95nr_block_0019	erm(46)_1	erm(46)	resfinder	2021-
 GMGC10.008_222_153.SCLAV_1890	GMGC10.95nr_block_0019	lnu(G)_1	lnu(G)	resfinder	2021-Mar-27	KX470419	abricate	abricate 1.0.1	98.51			1	804					+		100.0						Lincomycin			ARO:3004085	ARO:0000046	ARO:0000017
 GMGC10.008_362_797.OXA	GMGC10.95nr_block_0019	blaOXA-22_1	blaOXA-22	resfinder	2021-Mar-27	AF064820	abricate	abricate 1.0.1	92.0			4	828					+		100.0						Amoxicillin;Ampicillin;Aztreonam;Cefepime;Piperacillin;Piperacillin+Tazobactam			ARO:3001417	ARO:0000032,ARO:0000056,ARO:3000008	ARO:3000007,ARO:3000007,ARO:3000007
 GMGC10.008_362_873.YBXI	GMGC10.95nr_block_0019	blaOXA-60d_1	blaOXA-60d	resfinder	2021-Mar-27	AY664506	abricate	abricate 1.0.1	100.0			1	816					+		100.0									ARO:3005326	ARO:0000020,ARO:0000056,ARO:3000008	ARO:3000007,ARO:3000007,ARO:3000007
-GMGC10.009_105_560.AADA	GMGC10.95nr_block_0019	aadA24_1	aadA24	resfinder	2021-Mar-27	AM711129	abricate	abricate 1.0.1	100.0			40	819					+		100.0						Streptomycin			ARO:3002621	ARO:0000039,ARO:0000040	ARO:0000016,ARO:0000016
+GMGC10.009_105_560.AADA	GMGC10.95nr_block_0019	aadA24_1	aadA24	resfinder	2021-Mar-27	AM711129	abricate	abricate 1.0.1	100.0			40	819					+		100.0						Streptomycin			ARO:3002601	ARO:0000039,ARO:0000040	ARO:0000016,ARO:0000016
 GMGC10.009_704_406.AADA	GMGC10.95nr_block_0019	ant(9)-Ia_1	ant(9)-Ia	resfinder	2021-Mar-27	X02588	abricate	abricate 1.0.1	94.1			1	780					+		99.62									ARO:3002630	ARO:0000039	ARO:0000016
 GMGC10.009_706_608.UNKNOWN	GMGC10.95nr_block_0019	blaOXA-209_1	blaOXA-209	resfinder	2021-Mar-27	JF268688	abricate	abricate 1.0.1	82.06			1	731					+		88.0									ARO:3001809	ARO:0000056	ARO:3000007
 GMGC10.010_454_812.YBXI	GMGC10.95nr_block_0019	blaOXA-54_1	blaOXA-54	resfinder	2021-Mar-27	AY500137	abricate	abricate 1.0.1	100.0			1	798					+		100.0						Amoxicillin;Amoxicillin+Clavulanic_acid;Ampicillin;Ampicillin+Clavulanic_acid;Imipenem;Piperacillin;Piperacillin+Tazobactam			ARO:3001812	ARO:0000020,ARO:0000056,ARO:3000008	ARO:3000007,ARO:3000007,ARO:3000007
@@ -753,7 +753,7 @@ GMGC10.026_771_731.UNKNOWN	GMGC10.95nr_block_0021	blaGOB-13_1	blaGOB-13	resfinde
 GMGC10.026_771_858.UNKNOWN	GMGC10.95nr_block_0021	blaCME-1_1	blaCME-1	resfinder	2021-Mar-27	AJ006275	abricate	abricate 1.0.1	87.68			1	885					+		99.66									ARO:3004775	ARO:3000008	ARO:3000007
 GMGC10.026_777_350.UNKNOWN	GMGC10.95nr_block_0021	blaCME-1_1	blaCME-1	resfinder	2021-Mar-27	AJ006275	abricate	abricate 1.0.1	97.07			1	888					+		100.0									ARO:3004775	ARO:3000008	ARO:3000007
 GMGC10.026_779_337.UNKNOWN	GMGC10.95nr_block_0021	blaGOB-7_1	blaGOB-7	resfinder	2021-Mar-27	AF189297	abricate	abricate 1.0.1	99.47			64	819					+		100.0									ARO:3005696	ARO:0000020,ARO:0000032,ARO:3000008	ARO:3000007,ARO:3000007,ARO:3000007
-GMGC10.027_771_681.BLA	GMGC10.95nr_block_0021	blaCTX-M-63_1	blaCTX-M-63	resfinder	2021-Mar-27	EU660216	abricate	abricate 1.0.1	100.0			1	873					+		100.0						Amoxicillin;Ampicillin;Aztreonam;Cefepime;Cefotaxime;Ceftazidime;Ceftriaxone;Piperacillin;Ticarcillin			ARO:3001924	ARO:0000032	ARO:3000007
+GMGC10.027_771_681.BLA	GMGC10.95nr_block_0021	blaCTX-M-63_1	blaCTX-M-63	resfinder	2021-Mar-27	EU660216	abricate	abricate 1.0.1	100.0			1	873					+		100.0						Amoxicillin;Ampicillin;Aztreonam;Cefepime;Cefotaxime;Ceftazidime;Ceftriaxone;Piperacillin;Ticarcillin					
 GMGC10.031_929_892.BLA	GMGC10.95nr_block_0021	blaNMC-A_1	blaNMC-A	resfinder	2021-Mar-27	AJ536087	abricate	abricate 1.0.1	94.31			1	879					+		100.0									ARO:3003589	ARO:0000008,ARO:0000020,ARO:0000058,ARO:3000637	ARO:3000007,ARO:3000007,ARO:3000007,ARO:3000007
 GMGC10.033_249_710.BLA	GMGC10.95nr_block_0021	blaSME-2_1	blaSME-2	resfinder	2021-Mar-27	AF275256	abricate	abricate 1.0.1	100.0			1	885					+		100.0									ARO:3002380	ARO:0000020	ARO:3000007
 GMGC10.034_566_540.AACC	GMGC10.95nr_block_0021	aac(3)-VIIa_1	aac(3)-VIIa	resfinder	2021-Mar-27	M22999	abricate	abricate 1.0.1	94.0			1	867					+		100.0									ARO:3002541	ARO:3000657	ARO:0000016
@@ -767,7 +767,7 @@ GMGC10.036_938_985.BLA	GMGC10.95nr_block_0021	blaBKC-1_1	blaBKC-1	resfinder	2021
 GMGC10.037_085_608.AACC	GMGC10.95nr_block_0021	aac(3)-VIII_1	aac(3)-VIII	resfinder	2021-Mar-27	AB211959	abricate	abricate 1.0.1	99.77			1	864					+		100.0									ARO:3002542	ARO:0000005	ARO:0000016
 GMGC10.037_640_871.APHD	GMGC10.95nr_block_0021	aph(6)-Ib_1	aph(6)-Ib	resfinder	2021-Mar-27	X05648	abricate	abricate 1.0.1	80.97			1	878					+		94.48						Streptomycin			ARO:3002658	ARO:0000040	ARO:0000016
 GMGC10.037_977_769.UNKNOWN	GMGC10.95nr_block_0021	blaCME-1_1	blaCME-1	resfinder	2021-Mar-27	AJ006275	abricate	abricate 1.0.1	85.63			71	891					+		92.45									ARO:3004775	ARO:3000008	ARO:3000007
-GMGC10.038_139_710.BLA	GMGC10.95nr_block_0021	blaCARB-4_1	blaCARB-4	resfinder	2021-Mar-27	FJ785525	abricate	abricate 1.0.1	99.65			1	867					+		100.0						Ampicillin;Amoxicillin;Piperacillin			ARO:3002243	ARO:3000008	ARO:3000007
+GMGC10.038_139_710.BLA	GMGC10.95nr_block_0021	blaCARB-4_1	blaCARB-4	resfinder	2021-Mar-27	FJ785525	abricate	abricate 1.0.1	99.65			1	867					+		100.0						Ampicillin;Amoxicillin;Piperacillin					
 GMGC10.038_221_062.BLA	GMGC10.95nr_block_0021	blaCARB-9_1	blaCARB-9	resfinder	2021-Mar-27	AY248038	abricate	abricate 1.0.1	99.65			1	867					+		100.0						Ampicillin;Amoxicillin;Piperacillin			ARO:3002248	ARO:3000008	ARO:3000007
 GMGC10.040_295_342.UNKNOWN	GMGC10.95nr_block_0021	blaOXA-152_1	blaOXA-152	resfinder	2021-Mar-27	KP771980	abricate	abricate 1.0.1	81.03			136	873					+		86.01									ARO:3001457	ARO:0000020,ARO:0000056,ARO:3000008	ARO:3000007,ARO:3000007,ARO:3000007
 GMGC10.041_088_390.DIMT1	GMGC10.95nr_block_0021	erm(O)_1	erm(O)	resfinder	2021-Mar-27	M74717	abricate	abricate 1.0.1	82.12			1	775					+		98.21						Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S			ARO:3004652	ARO:0000006,ARO:0000046,ARO:3000145	ARO:0000000,ARO:0000000,ARO:0000017