├── .gitattributes ├── .gitignore ├── BENCHMARKING.md ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── images └── pyhmmer-benchmarking.jpeg ├── pykofamsearch.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── requires.txt └── top_level.txt ├── pykofamsearch ├── __init__.py ├── __pycache__ │ └── version.cpython-310.pyc ├── pykofamsearch.py ├── reformat_pykofamsearch.py ├── serialize_kofam_models.py └── subset_serialized_models.py ├── requirements.txt ├── setup.py └── test ├── benchmark.sh ├── diamond_output.query.list ├── diamond_output.tsv ├── kofamscan_output.sig.tsv.gz ├── kofamscan_output.tsv.gz ├── pykofamsearch_output.reformatted.best_hits_only.tsv.gz ├── pykofamsearch_output.reformatted.tsv.gz ├── pykofamsearch_output.tsv.gz ├── test.diamond_swissprot.faa ├── test.diamond_swissprot.pykofamsearch.tsv ├── test.enzymes.pykofamsearch.tsv ├── test.faa ├── test.t-0.5.tsv ├── test.tsv ├── test_noheader.tsv └── test_parts ├── stdin.part_001.fasta ├── 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