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Fix AttributeError when AMRFinderPlus subclass is missing from CARD conversion table #34

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Fix AttributeError when AMRFinderPlus subclass is missing from CARD conversion table #34

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12 changes: 10 additions & 2 deletions src/amrrules/genotype_parser.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from typing import Any, Optional
import re
import warnings
from amrrules import __version__
from amrrules.utils import aa_conversion, minimal_columns, full_columns

Expand Down Expand Up @@ -397,8 +398,15 @@ def _assign_drug_from_rule(self, card_drug_map):
self.drug_class = 'penicillin beta-lactam'

def _assign_drug_from_amrfp(self, card_amrfp_conversion):
self.drug = card_amrfp_conversion.get(self.amrfp_subclass).get('drug', '-')
self.drug_class = card_amrfp_conversion.get(self.amrfp_subclass).get('class', '-')
conversion = card_amrfp_conversion.get(self.amrfp_subclass)
if conversion is None:
# the amrfp_to_card_drugs_classes.txt lookup table is maintained by hand and can
# lag behind the AMRFinderPlus/NCBI database, so an unmapped subclass shouldn't crash the run
warnings.warn(f"AMRFinderPlus subclass '{self.amrfp_subclass}' was not found in the AMRFP-to-CARD "
f"conversion table. Falling back to 'unassigned markers' for this marker.")
conversion = {}
self.drug = conversion.get('drug', '-')
self.drug_class = conversion.get('class', '-')
# if the drug_class is '-', set to 'unassigned markers'
if self.drug_class == '-':
self.drug_class = 'unassigned markers'
Expand Down