altar-popfreq 0.2.0__tar.gz

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Files changed (17) hide show
  1. altar_popfreq-0.2.0/.gitignore +33 -0
  2. altar_popfreq-0.2.0/LICENSE +21 -0
  3. altar_popfreq-0.2.0/PKG-INFO +656 -0
  4. altar_popfreq-0.2.0/README.md +630 -0
  5. altar_popfreq-0.2.0/altar_popfreq/__init__.py +43 -0
  6. altar_popfreq-0.2.0/altar_popfreq/build_dataset.py +597 -0
  7. altar_popfreq-0.2.0/altar_popfreq/py.typed +0 -0
  8. altar_popfreq-0.2.0/altar_popfreq/source.py +500 -0
  9. altar_popfreq-0.2.0/altar_popfreq/warehouse.py +120 -0
  10. altar_popfreq-0.2.0/pyproject.toml +59 -0
  11. altar_popfreq-0.2.0/tests/fixtures/gnomad.genomes.v4.1.sites.synthetic.vcf +44 -0
  12. altar_popfreq-0.2.0/tests/fixtures/gnomad.joint.v4.1.sites.synthetic.vcf +38 -0
  13. altar_popfreq-0.2.0/tests/test_build_dataset.py +842 -0
  14. altar_popfreq-0.2.0/tests/test_published_contract.py +51 -0
  15. altar_popfreq-0.2.0/tests/test_pull.py +124 -0
  16. altar_popfreq-0.2.0/tests/test_run_spec.py +222 -0
  17. altar_popfreq-0.2.0/tests/test_source.py +855 -0
altar_popfreq-0.2.0/.gitignore ADDED
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+ *.pyc
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+ *~
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+ **/__pycache__/*
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+ *.swp
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+ .vscode/
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+ .idea/
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+ .DS_Store
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+ .env*
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+ .mypy_cache/
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+ .ruff_cache/
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+ .pytest_cache/
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+ .coverage
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+ htmlcov/
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+ coverage.xml
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+ pytest.xml
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+ .hypothesis/
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+ .python-version
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+ .venv
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+ .venv-*/
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+ *.egg-info/
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+ build/
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+ dist/
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+ site/
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+ *.sqlite3
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+ *.log
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+
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+ # Generated variant indexes and datasets. The small canonical gene table is tracked.
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+ altar/altar/variants/data/ccres.dnatree
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+ altar/altar/variants/data/region_annotations.parquet
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+ altar/altar/variants/data/variants.pkl.gz
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+ altar/altar/variants/data/region_provenance.json
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+ altar/altar/variants/data/raw/
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+
altar_popfreq-0.2.0/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2026 Riya Sinha
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.