Add HamronizationNormalizer #85
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Vedanth-Ramji
commented
Feb 4, 2025
Vedanth-Ramji
commented
- Removed the is_hamronized property for all Normalizers.
- All hamronized results now go through the HamronizationNormalizer class.
- HamronizationNormalizer reads a hamronized file line by line, procures input genes, and loads all ARO mapping tables to support hamronized results that combine the outputs from multiple tools and databases.
- Removed the `is_hamronized` property for all Normalizers. - All hamronized results now go through the `HamronizationNormalizer` class. - HamronizationNormalizer reads a hamronized file line by line, procures input genes, and loads all ARO mapping tables to support hamronized results that combine the outputs from multiple tools and databases.
- Removed '--hamronized' flag for CLI - Added `hamronization` as a tool option which invokes `HamronizationNormalizer`. `hamronization` doesn't required `--db` option, and is intended to be used in the following manner: "argnorm hamronization -i PATH_TO_INPUT -o PATH_TO_OUTPUT"
- hAMRonized result from https://raw.githubusercontent.com/ewissel/hAMRoaster/refs/heads/main/study_data/ham_sum.tsv - Used to test HarmonizationNormalizer on a hamronized file with the combined outputs from different ARG annotation tools (along with their respective databases)
- Updated 'run_argnorm.py' to support the 'hamronization' tool option rather than the '--hamronization' flag
- Removed '@pytest.mark.parametrize('hamronized', [True, False])' in 'test_normalizers.py'. Added test_hamronization_normalizer() which normalizes and tests every file in examples/hamronized
- Added normalized output of combined_hamronization.tsv
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Thanks! I will look more closely at the implementation later, but a few UX suggestions:
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Merged manually (on command line) |
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