genal-python 1.4.7__tar.gz → 1.4.8__tar.gz

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 (43) hide show
  1. {genal_python-1.4.7 → genal_python-1.4.8}/PKG-INFO +1 -1
  2. {genal_python-1.4.7 → genal_python-1.4.8}/genal/__init__.py +1 -1
  3. {genal_python-1.4.7 → genal_python-1.4.8}/genal/lift.py +2 -0
  4. {genal_python-1.4.7 → genal_python-1.4.8}/pyproject.toml +1 -1
  5. {genal_python-1.4.7 → genal_python-1.4.8}/.DS_Store +0 -0
  6. {genal_python-1.4.7 → genal_python-1.4.8}/.gitignore +0 -0
  7. {genal_python-1.4.7 → genal_python-1.4.8}/.readthedocs.yaml +0 -0
  8. {genal_python-1.4.7 → genal_python-1.4.8}/Genal_flowchart.png +0 -0
  9. {genal_python-1.4.7 → genal_python-1.4.8}/LICENSE +0 -0
  10. {genal_python-1.4.7 → genal_python-1.4.8}/README.md +0 -0
  11. {genal_python-1.4.7 → genal_python-1.4.8}/docs/.DS_Store +0 -0
  12. {genal_python-1.4.7 → genal_python-1.4.8}/docs/Makefile +0 -0
  13. {genal_python-1.4.7 → genal_python-1.4.8}/docs/make.bat +0 -0
  14. {genal_python-1.4.7 → genal_python-1.4.8}/docs/requirements.txt +0 -0
  15. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/.DS_Store +0 -0
  16. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/Images/Genal_flowchart.png +0 -0
  17. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/Images/MR_plot_SBP_AS.png +0 -0
  18. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/Images/genal_logo.png +0 -0
  19. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/api.md +0 -0
  20. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/concepts.md +0 -0
  21. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/conf.py +0 -0
  22. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/faq.md +0 -0
  23. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/index.md +0 -0
  24. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/introduction.md +0 -0
  25. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/methods.md +0 -0
  26. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/setup.md +0 -0
  27. {genal_python-1.4.7 → genal_python-1.4.8}/docs/source/workflows.md +0 -0
  28. {genal_python-1.4.7 → genal_python-1.4.8}/genal/Geno.py +0 -0
  29. {genal_python-1.4.7 → genal_python-1.4.8}/genal/MR.py +0 -0
  30. {genal_python-1.4.7 → genal_python-1.4.8}/genal/MR_tools.py +0 -0
  31. {genal_python-1.4.7 → genal_python-1.4.8}/genal/MRpresso.py +0 -0
  32. {genal_python-1.4.7 → genal_python-1.4.8}/genal/association.py +0 -0
  33. {genal_python-1.4.7 → genal_python-1.4.8}/genal/clump.py +0 -0
  34. {genal_python-1.4.7 → genal_python-1.4.8}/genal/colocalization.py +0 -0
  35. {genal_python-1.4.7 → genal_python-1.4.8}/genal/constants.py +0 -0
  36. {genal_python-1.4.7 → genal_python-1.4.8}/genal/extract_prs.py +0 -0
  37. {genal_python-1.4.7 → genal_python-1.4.8}/genal/genes.py +0 -0
  38. {genal_python-1.4.7 → genal_python-1.4.8}/genal/geno_tools.py +0 -0
  39. {genal_python-1.4.7 → genal_python-1.4.8}/genal/proxy.py +0 -0
  40. {genal_python-1.4.7 → genal_python-1.4.8}/genal/snp_query.py +0 -0
  41. {genal_python-1.4.7 → genal_python-1.4.8}/genal/tools.py +0 -0
  42. {genal_python-1.4.7 → genal_python-1.4.8}/genal_logo.png +0 -0
  43. {genal_python-1.4.7 → genal_python-1.4.8}/gitignore +0 -0
{genal_python-1.4.7 → genal_python-1.4.8}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: genal-python
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- Version: 1.4.7
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+ Version: 1.4.8
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  Summary: A python toolkit for polygenic risk scoring and mendelian randomization.
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  Author-email: Cyprien Rivier <riviercyprien@gmail.com>
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  Requires-Python: >=3.8
{genal_python-1.4.7 → genal_python-1.4.8}/genal/__init__.py RENAMED
@@ -5,7 +5,7 @@ from .geno_tools import Combine_Geno
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  from .genes import filter_by_gene_func
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  from .constants import CONFIG_DIR
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- __version__ = "1.4.7"
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+ __version__ = "1.4.8"
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  config_path = os.path.join(CONFIG_DIR, "config.json")
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{genal_python-1.4.7 → genal_python-1.4.8}/genal/lift.py RENAMED
@@ -51,6 +51,8 @@ def lift_data(
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  # Prepare the data for lifting: handle missing values in CHR, POS columns
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  nrows = data.shape[0]
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  data.dropna(subset=["CHR", "POS"], inplace=True)
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+ # Remove absurd positions
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+ data = data[data.POS < 300_000_000]
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  data.reset_index(drop=True, inplace=True)
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  n_na = nrows - data.shape[0]
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  if n_na:
{genal_python-1.4.7 → genal_python-1.4.8}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
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  [project]
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  name = "genal-python" # Updated name for PyPI
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- version = "1.4.7"
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+ version = "1.4.8"
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  authors = [{name = "Cyprien Rivier", email = "riviercyprien@gmail.com"}]
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  description = "A python toolkit for polygenic risk scoring and mendelian randomization."
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  readme = "README.md"
{genal_python-1.4.7 → genal_python-1.4.8}/.DS_Store RENAMED
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{genal_python-1.4.7 → genal_python-1.4.8}/.gitignore RENAMED
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{genal_python-1.4.7 → genal_python-1.4.8}/LICENSE RENAMED
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{genal_python-1.4.7 → genal_python-1.4.8}/README.md RENAMED
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{genal_python-1.4.7 → genal_python-1.4.8}/docs/Makefile RENAMED
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{genal_python-1.4.7 → genal_python-1.4.8}/docs/make.bat RENAMED
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{genal_python-1.4.7 → genal_python-1.4.8}/genal/Geno.py RENAMED
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{genal_python-1.4.7 → genal_python-1.4.8}/genal/MR.py RENAMED
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{genal_python-1.4.7 → genal_python-1.4.8}/gitignore RENAMED
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