sai-pg 1.0.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (30) hide show
  1. sai/__init__.py +18 -0
  2. sai/__main__.py +73 -0
  3. sai/parsers/__init__.py +18 -0
  4. sai/parsers/argument_validation.py +169 -0
  5. sai/parsers/outlier_parser.py +76 -0
  6. sai/parsers/plot_parser.py +152 -0
  7. sai/parsers/score_parser.py +241 -0
  8. sai/sai.py +315 -0
  9. sai/stats/__init__.py +18 -0
  10. sai/stats/features.py +302 -0
  11. sai/utils/__init__.py +22 -0
  12. sai/utils/generators/__init__.py +23 -0
  13. sai/utils/generators/chunk_generator.py +148 -0
  14. sai/utils/generators/data_generator.py +49 -0
  15. sai/utils/generators/window_generator.py +250 -0
  16. sai/utils/genomic_dataclasses.py +46 -0
  17. sai/utils/multiprocessing/__init__.py +22 -0
  18. sai/utils/multiprocessing/mp_manager.py +251 -0
  19. sai/utils/multiprocessing/mp_pool.py +73 -0
  20. sai/utils/preprocessors/__init__.py +23 -0
  21. sai/utils/preprocessors/chunk_preprocessor.py +152 -0
  22. sai/utils/preprocessors/data_preprocessor.py +94 -0
  23. sai/utils/preprocessors/feature_preprocessor.py +211 -0
  24. sai/utils/utils.py +689 -0
  25. sai_pg-1.0.0.dist-info/METADATA +44 -0
  26. sai_pg-1.0.0.dist-info/RECORD +30 -0
  27. sai_pg-1.0.0.dist-info/WHEEL +5 -0
  28. sai_pg-1.0.0.dist-info/entry_points.txt +2 -0
  29. sai_pg-1.0.0.dist-info/licenses/LICENSE +674 -0
  30. sai_pg-1.0.0.dist-info/top_level.txt +1 -0
sai_pg-1.0.0.dist-info/METADATA ADDED
@@ -0,0 +1,44 @@
1
+ Metadata-Version: 2.4
2
+ Name: sai-pg
3
+ Version: 1.0.0
4
+ Summary: A Python Package for Statistics for Adaptive Introgression
5
+ Home-page: https://github.com/xin-huang/sai
6
+ Author: Xin Huang
7
+ Author-email: xinhuang.res@gmail.com
8
+ License: GPLv3
9
+ Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
10
+ Classifier: Programming Language :: Python
11
+ Classifier: Programming Language :: Python :: 3.9
12
+ Requires-Python: ==3.9.19
13
+ Description-Content-Type: text/markdown
14
+ License-File: LICENSE
15
+ Requires-Dist: matplotlib==3.9.1
16
+ Requires-Dist: natsort==8.4.0
17
+ Requires-Dist: numpy==1.26.4
18
+ Requires-Dist: pandas==2.2.1
19
+ Requires-Dist: pysam==0.23.0
20
+ Requires-Dist: scikit-allel==1.3.7
21
+ Requires-Dist: scipy==1.12.0
22
+ Dynamic: author
23
+ Dynamic: author-email
24
+ Dynamic: classifier
25
+ Dynamic: description
26
+ Dynamic: description-content-type
27
+ Dynamic: home-page
28
+ Dynamic: license
29
+ Dynamic: license-file
30
+ Dynamic: requires-dist
31
+ Dynamic: requires-python
32
+ Dynamic: summary
33
+
34
+ # SAI
35
+
36
+ [![license](https://img.shields.io/badge/license-GPL%20v3-black.svg?style=flat-square)](LICENSE)
37
+ [![language](http://img.shields.io/badge/language-Python-blue.svg?style=flat-square)](https://www.python.org/)
38
+ [![build status](https://img.shields.io/github/actions/workflow/status/xin-huang/sai/build.yaml?branch=main&style=flat-square)](https://github.com/xin-huang/sai/actions)
39
+ [![codecov](https://img.shields.io/codecov/c/github/xin-huang/sai?style=flat-square)](https://app.codecov.io/gh/xin-huang/sai)
40
+ [![docs](https://img.shields.io/github/actions/workflow/status/xin-huang/sai/pages/pages-build-deployment?style=flat-square&label=docs)](https://github.com/xin-huang/sai/deployments/github-pages)
41
+
42
+ A Python Package for **S**tatistics for **A**daptive **I**ntrogression
43
+
44
+ The manual can be found [here](https://xin-huang.github.io/sai).
sai_pg-1.0.0.dist-info/RECORD ADDED
@@ -0,0 +1,30 @@
1
+ sai/__init__.py,sha256=ZLPiBk86c9R8ZFx9y5VF7Up2v4JS8WsEMfsVNlj7nXY,724
2
+ sai/__main__.py,sha256=WJMDikIfZh-g9j9pl0o6sZqVb4llQpUhBcJbn4-9pvE,2058
3
+ sai/sai.py,sha256=ffPTVxKMoLFX-zr9lsiU-p5KDict9glSTMiNcgWVtsw,9969
4
+ sai/parsers/__init__.py,sha256=ZLPiBk86c9R8ZFx9y5VF7Up2v4JS8WsEMfsVNlj7nXY,724
5
+ sai/parsers/argument_validation.py,sha256=OzkE9Ayr3KCB8rSP8mXnfx4aNOeJuEEFfit9q7RbURU,4374
6
+ sai/parsers/outlier_parser.py,sha256=Qw0E_1zFxfYoynnYJ1scbQHEpPVaHwTCPtPe3n643I4,2354
7
+ sai/parsers/plot_parser.py,sha256=C4uGH96th8Yj7KN7onkE6xTqYa8K7EiU-21xgZYDNZE,4556
8
+ sai/parsers/score_parser.py,sha256=qZ6mLBHd2QwAb2V0QaOgzBkgpb6mZv_rdDckwzN0e38,8604
9
+ sai/stats/__init__.py,sha256=ZLPiBk86c9R8ZFx9y5VF7Up2v4JS8WsEMfsVNlj7nXY,724
10
+ sai/stats/features.py,sha256=7CI9i3csVH9sXryWGB0uLSJB6BbM9gJtA1IPN2EeT0k,11844
11
+ sai/utils/__init__.py,sha256=B3ZcC1ALSWieGHPiqXKBFQRTrnlTX4TaHc3tCx9fj0w,782
12
+ sai/utils/genomic_dataclasses.py,sha256=HBYp2dehdW_y3Pd6Un8XFMnN1Odg1EiZb9ci1syIibU,1443
13
+ sai/utils/utils.py,sha256=Nnb1tPHWk9vmlRmUJ65_FEmLfDEsT41HZ9WvJ0ps7Vs,23127
14
+ sai/utils/generators/__init__.py,sha256=hpE4PUQIOZQXzdpSx7dEllecDoOfxIWXNu1-WHa_VcM,858
15
+ sai/utils/generators/chunk_generator.py,sha256=Jh0wDOR6Z5PXlzOTncmY-pr9PotnmfiWTZQL2aaVGAs,4565
16
+ sai/utils/generators/data_generator.py,sha256=bVz9KPjJSL4becTsVZ-zH4i40y5UDA0JJOtzbwf5n84,1635
17
+ sai/utils/generators/window_generator.py,sha256=G8aMmJbB8uWLNaoJAGSeBFTCvAib7DdWvbXDk9JvDdM,9066
18
+ sai/utils/multiprocessing/__init__.py,sha256=mI_iVjOJschKjIcneo99utCMVjR0K3UpEjA_PMcmLm4,790
19
+ sai/utils/multiprocessing/mp_manager.py,sha256=xbgje4Fi4U9WD7eqMlUkTLKLQ9aNV_hIG7nTYvniGFk,10263
20
+ sai/utils/multiprocessing/mp_pool.py,sha256=wqgp7E7fU2MXKsv7d8kpIp40SLjqS8voxbB_FkVwczA,2273
21
+ sai/utils/preprocessors/__init__.py,sha256=q25uXnq4jTrIVBbl1HFv3ZgEV0d79fCMp4tTZrq4vsM,878
22
+ sai/utils/preprocessors/chunk_preprocessor.py,sha256=mNmc22PmIRZZjYoyktxKSRGSGzN_e1Cyi392VxTbtWc,5204
23
+ sai/utils/preprocessors/data_preprocessor.py,sha256=XSQN_kXUfyCtIpqIf7TcqWIPcSk8kynHPH-KY9gh5VY,3595
24
+ sai/utils/preprocessors/feature_preprocessor.py,sha256=Kmc7VsO9YJcbFwWk-Jha5Rzq7gZou1pwYh93Wpd9r5o,7143
25
+ sai_pg-1.0.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
26
+ sai_pg-1.0.0.dist-info/METADATA,sha256=e16SXHsIZBXK5EtJDbDhyPJdEXcKes88sCNPls_s3y4,1789
27
+ sai_pg-1.0.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
28
+ sai_pg-1.0.0.dist-info/entry_points.txt,sha256=uK34frE2UhEDNa5ISbGOtjF2HGAXF5uG_EgMocesEPs,42
29
+ sai_pg-1.0.0.dist-info/top_level.txt,sha256=Kvf-0z0sZYQbLuM6ta183EOzD37k3VZbRH-h7HXntR0,4
30
+ sai_pg-1.0.0.dist-info/RECORD,,
sai_pg-1.0.0.dist-info/WHEEL ADDED
@@ -0,0 +1,5 @@
1
+ Wheel-Version: 1.0
2
+ Generator: setuptools (78.1.0)
3
+ Root-Is-Purelib: true
4
+ Tag: py3-none-any
5
+
sai_pg-1.0.0.dist-info/entry_points.txt ADDED
@@ -0,0 +1,2 @@
1
+ [console_scripts]
2
+ sai = sai.__main__:main