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Adding Pf9 functionality#1236

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jonbrenas merged 4 commits intomalariagen:masterfrom
nw20:add_pf9
Apr 1, 2026
Merged

Adding Pf9 functionality#1236
jonbrenas merged 4 commits intomalariagen:masterfrom
nw20:add_pf9

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@nw20 nw20 commented Mar 27, 2026

Adding a Pf9 class for accessing the Pf9 data release.

Changes/additions:

  1. modify malariagen_data/__init__.py - add pf9 import
  2. create malariagen_data/pf9.py - based on Pf7 template (no S3 mentions)
  3. create malariagen_data/pf9_config.json - based on Pf8 template
  4. modify malariagen_data/plasmodium.py - add 'low_memory = False' to csv import to prevent warnings
  5. create tests/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:

  1. test_pf7, test_pf8, test_pf9.py all run and passed
  2. test_plasmodium.py passed
  3. run mypy malariagen_data tests --ignore-missing-imports no issues found
  4. pre-commit hooks passed

@nw20 nw20 requested a review from ahernank March 27, 2026 11:17
@nw20 nw20 requested a review from jonbrenas March 31, 2026 15:59
@jonbrenas jonbrenas merged commit 27e4283 into malariagen:master Apr 1, 2026
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2 participants