RFCT removed special casing for resfinder manual curation

- Note: code to integrate manual curation now removes duplicate ARO mappings. This has corrected a MEGARes annotation (GMGC10.027_903_362.EMRE) which had a one to many ARO mapping. Better manual curation for MEGARes will be present in the version after v0.3.0 when MEGARes will be investigated to check for CDSs, gene clusters and RC genes.
BigDataBiology · Apr 25, 2024 · de775cd · de775cd
1 parent d9ea531
commit de775cd
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Showing 2 changed files with 10 additions and 16 deletions.
diff --git a/argnorm/lib.py b/argnorm/lib.py
@@ -17,24 +17,18 @@ def is_number(num):
     return True
 
 def get_aro_mapping_table(database):
-    df = pd.read_csv(os.path.join(_ROOT, 'data', f'{database}_ARO_mapping.tsv'), sep='\t')
+    aro_mapping_table = pd.read_csv(os.path.join(_ROOT, 'data', f'{database}_ARO_mapping.tsv'), sep='\t')
 
     manual_curation = pd.read_csv(os.path.join(_ROOT, 'data/manual_curation', f'{database}_curation.tsv'), sep='\t')
-    manual_curation['Database'] = df['Database']
-    aro_mapping_table = df
+    manual_curation['Database'] = aro_mapping_table['Database']
 
-    if database != 'resfinder':
-        aro_mapping_table = pd.concat([df, manual_curation])
-    else:
-        # Handle gene clusters and reverse complements
-        aro_mapping_table = aro_mapping_table.drop_duplicates(subset=['Original ID'], ignore_index=True).set_index('Original ID')
-
-        for i in manual_curation['Original ID']:
-            if i in aro_mapping_table.index:
-                aro_mapping_table.loc[i, 'ARO'] = manual_curation.set_index('Original ID').loc[i, 'ARO']
-                aro_mapping_table.loc[i, 'Gene Name in CARD'] = manual_curation.set_index('Original ID').loc[i, 'Gene Name in CARD']
-            else:
-                aro_mapping_table.loc[i] = manual_curation.set_index('Original ID').loc[i]
+    aro_mapping_table = aro_mapping_table.drop_duplicates(subset=['Original ID'], ignore_index=True).set_index('Original ID')
+    for i in manual_curation['Original ID']:
+        if i in aro_mapping_table.index:
+            aro_mapping_table.loc[i, 'ARO'] = manual_curation.set_index('Original ID').loc[i, 'ARO']
+            aro_mapping_table.loc[i, 'Gene Name in CARD'] = manual_curation.set_index('Original ID').loc[i, 'Gene Name in CARD']
+        else:
+            aro_mapping_table.loc[i] = manual_curation.set_index('Original ID').loc[i]
 
     aro_mapping_table[TARGET_ARO_COL] = aro_mapping_table[TARGET_ARO_COL].map(lambda a: f'ARO:{int(a)}' if is_number(a) else a)
     return aro_mapping_table.reset_index()

diff --git a/outputs/hamronized/abricate.megares.tsv b/outputs/hamronized/abricate.megares.tsv
@@ -198,7 +198,7 @@ GMGC10.027_121_620.RBPA	GMGC10.95nr_block_0005	RBPA	Drugs:Rifampin:RNA-polymeras
 GMGC10.027_126_791.RBPA	GMGC10.95nr_block_0005	RBPA	Drugs:Rifampin:RNA-polymerase_binding_protein:RBPA	megares	2021-Mar-27	MEG_6047	abricate	abricate 1.0.1	91.39			1	302					+		87.54									ARO:3000245	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157
 GMGC10.027_135_808.MMR	GMGC10.95nr_block_0005	MMR	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MMR	megares	2021-Mar-27	MEG_3996	abricate	abricate 1.0.1	80.33			20	324					+		94.14									ARO:3005009	ARO:3005386	ARO:3005386
 GMGC10.027_272_655.SOXS	GMGC10.95nr_block_0005	SOXS	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	megares	2021-Mar-27	MEG_6551	abricate	abricate 1.0.1	80.29			36	314					+		86.11									ARO:3003511	ARO:0000036,ARO:3000385,ARO:3007045	ARO:0000001,ARO:0000001,ARO:3000387
-GMGC10.027_903_362.EMRE	GMGC10.95nr_block_0005	QACH	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACH	megares	2021-Mar-27	MEG_5847	abricate	abricate 1.0.1	87.65			1	324					+		100.0									ARO:3006954	ARO:0000020	ARO:3000007
+GMGC10.027_903_362.EMRE	GMGC10.95nr_block_0005	QACH	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACH	megares	2021-Mar-27	MEG_5847	abricate	abricate 1.0.1	87.65			1	324					+		100.0									ARO:3003836	ARO:3005386	ARO:3005386
 GMGC10.028_155_496.SOXS	GMGC10.95nr_block_0005	SOXS	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	megares	2021-Mar-27	MEG_6551	abricate	abricate 1.0.1	91.8			1	317					+		97.84									ARO:3003511	ARO:0000036,ARO:3000385,ARO:3007045	ARO:0000001,ARO:0000001,ARO:3000387
 GMGC10.028_171_025.RBPA	GMGC10.95nr_block_0005	RBPA	Drugs:Rifampin:RNA-polymerase_binding_protein:RBPA	megares	2021-Mar-27	MEG_6047	abricate	abricate 1.0.1	85.54			1	332					+		96.23									ARO:3000245	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157
 GMGC10.030_070_454.RBPA	GMGC10.95nr_block_0005	RBPA	Drugs:Rifampin:RNA-polymerase_binding_protein:RBPA	megares	2021-Mar-27	MEG_6047	abricate	abricate 1.0.1	92.77			1	332					+		96.23									ARO:3000245	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157