├── .github └── workflows │ └── python-package.yml ├── .gitignore ├── .readthedocs.yaml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── argnorm ├── __init__.py ├── argnorm_version.py ├── atomicwrite.py ├── cli.py ├── data │ ├── abricate_card_ARO_mapping.tsv │ ├── argannot_ARO_mapping.tsv │ ├── aro.obo │ ├── deeparg_ARO_mapping.tsv │ ├── groot_ARO_mapping.tsv │ ├── manual_curation │ │ ├── README.md │ │ ├── abricate_card_curation.tsv │ │ ├── argannot_curation.tsv │ │ ├── deeparg_curation.tsv │ │ ├── groot_curation.tsv │ │ ├── megares_curation.tsv │ │ ├── ncbi_curation.tsv │ │ ├── resfinder_curation.tsv │ │ ├── resfinderfg_curation.tsv │ │ └── sarg_curation.tsv │ ├── megares_ARO_mapping.tsv │ ├── ncbi_ARO_mapping.tsv │ ├── resfinder_ARO_mapping.tsv │ ├── resfinderfg_ARO_mapping.tsv │ └── sarg_ARO_mapping.tsv ├── drug_categorization.py ├── lib.py ├── normalize.py └── normalizers.py ├── db_harmonisation ├── .gitattributes ├── .gitignore ├── README.md ├── all_mismatched_hits.tsv ├── check_mapping_accuracy.py ├── construct_groot_mappings.py ├── construct_megares_mapping.py ├── crude_db_harmonisation.py ├── drug_classes │ ├── SARG_structure.tsv │ └── resfinder_antibiotic_classes.tsv ├── fasta.py ├── get_mapping_table.py ├── pixi.lock └── pixi.toml ├── docs ├── api.md ├── cli.md ├── images │ ├── argnorm_overview.svg │ └── argnorm_workflow.svg ├── index.md ├── requirements.txt └── whatsnew.md ├── examples ├── hamronized │ ├── abricate.argannot.tsv │ ├── abricate.card.tsv │ ├── abricate.megares.tsv │ ├── abricate.ncbi.hamronizationv4.tsv │ ├── abricate.ncbi.tsv │ ├── abricate.resfinder.tsv │ ├── abricate.resfinderfg.tsv │ ├── amrfinderplus.ncbi.orfs.v3.10.30.tsv │ ├── amrfinderplus.ncbi.orfs.v4.tsv │ ├── args-oap.sarg.orfs.tsv │ ├── args-oap.sarg.reads.tsv │ ├── combined_hamronization.tsv │ ├── combined_hamronization_full.tsv │ ├── deeparg.deeparg.orfs.tsv │ ├── groot.argannot.tsv │ ├── groot.card.tsv │ ├── groot.groot-core-db.tsv │ ├── groot.groot-db.tsv │ ├── groot.resfinder.tsv │ ├── resfinder.resfinder.orfs.tsv │ └── resfinder.resfinder.reads.tsv ├── raw │ ├── abricate.argannot.tsv │ ├── abricate.card.tsv │ ├── abricate.megares.tsv │ ├── abricate.ncbi.tsv │ ├── abricate.resfinder.tsv │ ├── amrfinderplus.ncbi.orfs.v3.10.30.tsv │ ├── amrfinderplus.ncbi.orfs.v4.tsv │ ├── args-oap.sarg.orfs.tsv │ ├── args-oap.sarg.reads.tsv │ ├── deeparg.deeparg.orfs.tsv │ ├── groot.argannot.tsv │ ├── groot.card.tsv │ ├── groot.groot-core-db.tsv │ ├── groot.groot-db.tsv │ ├── groot.resfinder.tsv │ ├── resfinder.resfinder.orfs.tsv │ └── resfinder.resfinder.reads.tsv └── scripts │ ├── README.md │ ├── get_amrfinderplus_v4.bash │ ├── get_combined_hamronization_example.sh │ └── get_groot_examples.py ├── integration_tests ├── .gitignore └── run_argnorm.py ├── mkdocs.yml ├── outputs ├── hamronized │ ├── abricate.argannot.tsv │ ├── abricate.card.tsv │ ├── abricate.megares.tsv │ ├── abricate.ncbi.hamronizationv4.tsv │ ├── abricate.ncbi.tsv │ ├── abricate.resfinder.tsv │ ├── abricate.resfinderfg.tsv │ ├── amrfinderplus.ncbi.orfs.v3.10.30.tsv │ ├── amrfinderplus.ncbi.orfs.v4.tsv │ ├── args-oap.sarg.reads.tsv │ ├── combined_hamronization.tsv │ ├── combined_hamronization_full.tsv │ ├── deeparg.deeparg.orfs.tsv │ ├── groot.argannot.tsv │ ├── groot.card.tsv │ ├── groot.groot-core-db.tsv │ ├── groot.groot-db.tsv │ ├── groot.resfinder.tsv │ ├── resfinder.resfinder.orfs.tsv │ └── resfinder.resfinder.reads.tsv └── raw │ ├── abricate.argannot.tsv │ ├── abricate.card.tsv │ ├── abricate.megares.tsv │ ├── abricate.ncbi.tsv │ ├── abricate.resfinder.tsv │ ├── amrfinderplus.ncbi.orfs.v3.10.30.tsv │ ├── amrfinderplus.ncbi.orfs.v4.tsv │ ├── args-oap.sarg.reads.tsv │ ├── deeparg.deeparg.orfs.tsv │ ├── groot.argannot.tsv │ ├── groot.card.tsv │ ├── groot.groot-core-db.tsv │ ├── groot.groot-db.tsv │ ├── groot.resfinder.tsv │ ├── resfinder.resfinder.orfs.tsv │ └── resfinder.resfinder.reads.tsv ├── pyproject.toml ├── tests ├── README.md ├── 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