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jonbrenas
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Apr 1, 2026
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Adding a
Pf9class for accessing the Pf9 data release.Changes/additions:
malariagen_data/__init__.py- add pf9 importmalariagen_data/pf9.py- based on Pf7 template (no S3 mentions)malariagen_data/pf9_config.json- based on Pf8 templatemalariagen_data/plasmodium.py- add 'low_memory = False' to csv import to prevent warningstests/integration/test_pf9.py- based on Pf8 test template, adapted for new Pf9 metadata columns and expected length. Removed 'variant_altlen' from expected variant columns, it was not present in Pf8 and is not in Pf9 so I have removed rather than comment out. A note from Pf8 on this "Since it is possible to calculate this value (altlen) from REF and ALT, we are not concerned about it now. Therefore, this field is excluded from data_vars after reading the Pf8 zarr file."Tests:
test_pf7,test_pf8,test_pf9.pyall run and passedtest_plasmodium.pypassedrun mypy malariagen_data tests --ignore-missing-importsno issues found