cwas-plus2 0.2.0__tar.gz

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Files changed (56) hide show
  1. cwas_plus2-0.2.0/Cargo.lock +371 -0
  2. cwas_plus2-0.2.0/Cargo.toml +3 -0
  3. cwas_plus2-0.2.0/LICENSE +21 -0
  4. cwas_plus2-0.2.0/PKG-INFO +26 -0
  5. cwas_plus2-0.2.0/cwas/__init__.py +0 -0
  6. cwas_plus2-0.2.0/cwas/__main__.py +10 -0
  7. cwas_plus2-0.2.0/cwas/annotation.py +305 -0
  8. cwas_plus2-0.2.0/cwas/argparser.py +1228 -0
  9. cwas_plus2-0.2.0/cwas/binomial_test.py +271 -0
  10. cwas_plus2-0.2.0/cwas/burden_shift.py +522 -0
  11. cwas_plus2-0.2.0/cwas/burden_test.py +373 -0
  12. cwas_plus2-0.2.0/cwas/categorization.py +334 -0
  13. cwas_plus2-0.2.0/cwas/cli.py +40 -0
  14. cwas_plus2-0.2.0/cwas/configuration.py +172 -0
  15. cwas_plus2-0.2.0/cwas/core/__init__.py +0 -0
  16. cwas_plus2-0.2.0/cwas/core/annotation/__init__.py +0 -0
  17. cwas_plus2-0.2.0/cwas/core/annotation/bed.py +128 -0
  18. cwas_plus2-0.2.0/cwas/core/annotation/vep.py +318 -0
  19. cwas_plus2-0.2.0/cwas/core/burden_test/__init__.py +0 -0
  20. cwas_plus2-0.2.0/cwas/core/burden_test/binomial.py +76 -0
  21. cwas_plus2-0.2.0/cwas/core/categorization/__init__.py +0 -0
  22. cwas_plus2-0.2.0/cwas/core/categorization/categorizer.py +721 -0
  23. cwas_plus2-0.2.0/cwas/core/categorization/category.py +56 -0
  24. cwas_plus2-0.2.0/cwas/core/categorization/parser.py +208 -0
  25. cwas_plus2-0.2.0/cwas/core/categorization/utils.py +28 -0
  26. cwas_plus2-0.2.0/cwas/core/common.py +164 -0
  27. cwas_plus2-0.2.0/cwas/core/configuration/__init__.py +0 -0
  28. cwas_plus2-0.2.0/cwas/core/configuration/create.py +85 -0
  29. cwas_plus2-0.2.0/cwas/core/configuration/settings.py +75 -0
  30. cwas_plus2-0.2.0/cwas/core/dawn/__init__.py +0 -0
  31. cwas_plus2-0.2.0/cwas/core/dawn/clustering.py +133 -0
  32. cwas_plus2-0.2.0/cwas/core/dawn/supernodeWGS.py +777 -0
  33. cwas_plus2-0.2.0/cwas/core/preparation/__init__.py +0 -0
  34. cwas_plus2-0.2.0/cwas/core/preparation/annotation.py +216 -0
  35. cwas_plus2-0.2.0/cwas/core/preparation/bedreader.py +38 -0
  36. cwas_plus2-0.2.0/cwas/correlation.py +401 -0
  37. cwas_plus2-0.2.0/cwas/dawn.py +408 -0
  38. cwas_plus2-0.2.0/cwas/effective_num_test.py +309 -0
  39. cwas_plus2-0.2.0/cwas/env.py +67 -0
  40. cwas_plus2-0.2.0/cwas/extract_variant.py +304 -0
  41. cwas_plus2-0.2.0/cwas/factory.py +42 -0
  42. cwas_plus2-0.2.0/cwas/permutation_test.py +250 -0
  43. cwas_plus2-0.2.0/cwas/preparation.py +96 -0
  44. cwas_plus2-0.2.0/cwas/risk_score.py +719 -0
  45. cwas_plus2-0.2.0/cwas/runnable.py +48 -0
  46. cwas_plus2-0.2.0/cwas/start.py +104 -0
  47. cwas_plus2-0.2.0/cwas/utils/__init__.py +0 -0
  48. cwas_plus2-0.2.0/cwas/utils/check.py +64 -0
  49. cwas_plus2-0.2.0/cwas/utils/cmd.py +93 -0
  50. cwas_plus2-0.2.0/cwas/utils/log.py +44 -0
  51. cwas_plus2-0.2.0/pyproject.toml +101 -0
  52. cwas_plus2-0.2.0/rust/Cargo.toml +16 -0
  53. cwas_plus2-0.2.0/rust/src/categorizer.rs +145 -0
  54. cwas_plus2-0.2.0/rust/src/intersection.rs +219 -0
  55. cwas_plus2-0.2.0/rust/src/lib.rs +16 -0
  56. cwas_plus2-0.2.0/rust/src/vcf_parser.rs +189 -0
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cwas_plus2-0.2.0/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2022 Minwoo Jeong
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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
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in all
13
+ copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21
+ SOFTWARE.
cwas_plus2-0.2.0/PKG-INFO ADDED
@@ -0,0 +1,26 @@
1
+ Metadata-Version: 2.4
2
+ Name: cwas-plus2
3
+ Version: 0.2.0
4
+ Requires-Dist: pandas>=2.1.0
5
+ Requires-Dist: numpy>=1.25.2
6
+ Requires-Dist: zarr>=2.16.1,<3
7
+ Requires-Dist: scipy>=1.13.1,<1.14
8
+ Requires-Dist: tqdm>=4.66.1
9
+ Requires-Dist: igraph>=0.10.8
10
+ Requires-Dist: matplotlib>=3.8.4,<3.9
11
+ Requires-Dist: seaborn>=0.13.2
12
+ Requires-Dist: parmap>=1.7.0
13
+ Requires-Dist: polars>=0.19.2
14
+ Requires-Dist: scikit-learn>=1.3.0
15
+ Requires-Dist: pysam>=0.22.1
16
+ Requires-Dist: numcodecs>=0.12.0
17
+ Requires-Dist: pyyaml>=6.0.1
18
+ Requires-Dist: python-dotenv>=1.0.0
19
+ Requires-Dist: pyarrow>=13,<15
20
+ Requires-Dist: adjusttext>=0.8
21
+ Requires-Dist: statsmodels>=0.14.1
22
+ Requires-Dist: scanpy>=1.10.1
23
+ Requires-Dist: python-glmnet-fix>=2.2.3
24
+ Requires-Dist: setuptools>=70.0.0,<75
25
+ License-File: LICENSE
26
+ Requires-Python: >=3.9, <3.13
cwas_plus2-0.2.0/cwas/__init__.py ADDED
File without changes
cwas_plus2-0.2.0/cwas/__main__.py ADDED
@@ -0,0 +1,10 @@
1
+ import cwas.cli
2
+
3
+
4
+ def main():
5
+ inst = cwas.cli.main()
6
+ inst.run()
7
+
8
+
9
+ if __name__ == "__main__":
10
+ main()