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clingen-data-model / clinvar-gk-python

Project for reading and normalizing ClinVar variants into GA4GH GKS forms
MIT License
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Port original gk-pilot python logic to initiate #1

Closed larrybabb closed 9 months ago

larrybabb commented 9 months ago

Port over any logic from the original python gk-pilot source code (and was later rebuilt in clojure in the same project).

larrybabb commented 9 months ago
  1. setup the repo clinvar-gk-python (to supercede clinvar-gk-pilot)
  2. configured packages (pyproject.toml)
  3. created baseline main.py script from portions of original python script that are useful (processline, args, ...)
  4. setup linter script for use by devs in local pre-commit hooks
  5. simplify main.py to read a gcp bucket file (and that's all)
  6. add logging
theferrit32 commented 9 months ago

I think this is all done except for (5). I would recommend closing and creating a separate issue to represent the work @toneillbroad is doing to read the variation_identity files.