AttributeError in _assign_drug_from_amrfp

[mikensubuga]

Thanks for creating this great resource!

A minor issue during the genome summary report generation phase. The interpreted genotype report is written successfully, but the summary report is never generated.

Command
amrrules --input amrfinder_results.tsv --output-prefix s_aureus --organism 's__Staphylococcus aureus'

Error

Matching markers to rules...
Traceback (most recent call last):
  File ".../bin/amrrules", line 6, in <module>
    sys.exit(main())
  File ".../amrrules/cli.py", line 62, in main
    rules_engine.run(args)
  File ".../amrrules/rules_engine.py", line 135, in run
    geno_obj = Genotype.from_result_row(g, card_amrfp=card_amrfp_conversion, amrfp_subclass=subclass, no_rule_interp=args.no_rule_interpretation)
  File ".../amrrules/genotype_parser.py", line 371, in from_result_row
    new_obj._assign_drug_from_amrfp(card_amrfp)
  File ".../amrrules/genotype_parser.py", line 400, in _assign_drug_from_amrfp
    self.drug = card_amrfp_conversion.get(self.amrfp_subclass).get('drug', '-')
AttributeError: 'NoneType' object has no attribute 'get'

I think the root cause is that AMRFinderPlus outputs FUSIDIC_ACID (with underscore) as the Subclass value for fusA point mutations (e.g. fusA_L461S, fusA_P404L, fusA_G451V). However, amrfp_to_card_drugs_classes.txt only contains FUSIDIC ACID (with a space), so card_amrfp_conversion.get('FUSIDIC_ACID') returns None, and the subsequent .get('drug', '-') call on None raises the AttributeError.

Thanks again for the resource!