gwaslab 3.4.36__tar.gz → 3.4.38__tar.gz

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Files changed (79) hide show
  1. {gwaslab-3.4.36/src/gwaslab.egg-info → gwaslab-3.4.38}/PKG-INFO +3 -3
  2. {gwaslab-3.4.36 → gwaslab-3.4.38}/pyproject.toml +3 -3
  3. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/__init__.py +1 -1
  4. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/data/formatbook.json +722 -721
  5. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/g_Log.py +8 -0
  6. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/g_Sumstats.py +80 -178
  7. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/g_SumstatsPair.py +6 -2
  8. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/g_Sumstats_summary.py +3 -3
  9. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/g_meta.py +13 -3
  10. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/g_version.py +2 -2
  11. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/hm_casting.py +29 -15
  12. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/hm_harmonize_sumstats.py +312 -159
  13. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/hm_rsid_to_chrpos.py +1 -1
  14. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/io_preformat_input.py +46 -37
  15. gwaslab-3.4.38/src/gwaslab/io_to_formats.py +602 -0
  16. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/qc_check_datatype.py +15 -1
  17. gwaslab-3.4.38/src/gwaslab/qc_fix_sumstats.py +1620 -0
  18. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_calculate_ldmatrix.py +29 -11
  19. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_gwascatalog.py +1 -1
  20. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_ldproxyfinder.py +1 -1
  21. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_process_h5.py +26 -17
  22. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_process_ref.py +3 -3
  23. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_run_coloc.py +26 -4
  24. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_in_convert_h2.py +1 -1
  25. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_in_fill_data.py +44 -5
  26. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_in_filter_value.py +122 -34
  27. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_in_get_density.py +2 -2
  28. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_in_get_sig.py +41 -9
  29. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_aux_quickfix.py +26 -21
  30. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_aux_reposition_text.py +7 -4
  31. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_aux_save_figure.py +6 -5
  32. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_compare_af.py +5 -5
  33. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_compare_effect.py +22 -5
  34. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_miamiplot2.py +28 -20
  35. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_mqqplot.py +214 -98
  36. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_qqplot.py +11 -8
  37. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_regionalplot.py +16 -9
  38. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_trumpetplot.py +15 -6
  39. {gwaslab-3.4.36 → gwaslab-3.4.38/src/gwaslab.egg-info}/PKG-INFO +3 -3
  40. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab.egg-info/requires.txt +1 -1
  41. gwaslab-3.4.36/src/gwaslab/io_to_formats.py +0 -469
  42. gwaslab-3.4.36/src/gwaslab/qc_fix_sumstats.py +0 -1383
  43. {gwaslab-3.4.36 → gwaslab-3.4.38}/LICENSE +0 -0
  44. {gwaslab-3.4.36 → gwaslab-3.4.38}/README.md +0 -0
  45. {gwaslab-3.4.36 → gwaslab-3.4.38}/setup.cfg +0 -0
  46. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/bd_common_data.py +0 -0
  47. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/bd_config.py +0 -0
  48. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/bd_download.py +0 -0
  49. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/bd_get_hapmap3.py +0 -0
  50. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/data/chrx_par/chrx_par_hg19.bed.gz +0 -0
  51. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/data/chrx_par/chrx_par_hg38.bed.gz +0 -0
  52. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz +0 -0
  53. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz +0 -0
  54. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz +0 -0
  55. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz +0 -0
  56. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/data/reference.json +0 -0
  57. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/g_Phenotypes.py +0 -0
  58. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/g_SumstatsT.py +0 -0
  59. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/g_vchange_status.py +0 -0
  60. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/io_read_ldsc.py +0 -0
  61. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/io_read_tabular.py +0 -0
  62. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/io_to_pickle.py +0 -0
  63. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/run_script.py +0 -0
  64. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_calculate_prs.py +0 -0
  65. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_plink_filter.py +0 -0
  66. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_run_2samplemr.py +0 -0
  67. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_run_clumping.py +0 -0
  68. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_ex_run_susie.py +0 -0
  69. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_in_calculate_gc.py +0 -0
  70. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_in_calculate_power.py +0 -0
  71. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/util_in_correct_winnerscurse.py +0 -0
  72. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_aux_annotate_plot.py +0 -0
  73. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_forestplot.py +0 -0
  74. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_miamiplot.py +0 -0
  75. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_rg_heatmap.py +0 -0
  76. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/viz_plot_stackedregional.py +0 -0
  77. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab.egg-info/SOURCES.txt +0 -0
  78. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab.egg-info/dependency_links.txt +0 -0
  79. {gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab.egg-info/top_level.txt +0 -0
{gwaslab-3.4.36/src/gwaslab.egg-info → gwaslab-3.4.38}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: gwaslab
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- Version: 3.4.36
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+ Version: 3.4.38
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  Summary: A collection of handy tools for GWAS SumStats
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  Author-email: Yunye <yunye@gwaslab.com>
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  Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -8,13 +8,13 @@ Project-URL: Github, https://github.com/Cloufield/gwaslab
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  Classifier: Programming Language :: Python :: 3
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  Classifier: License :: OSI Approved :: MIT License
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  Classifier: Operating System :: OS Independent
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- Requires-Python: <=3.10,>=3.8
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+ Requires-Python: <=3.10,>=3.9
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: pandas!=1.5,>=1.3
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  Requires-Dist: numpy>=1.21.2
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  Requires-Dist: matplotlib!=3.7.2,>=3.5
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- Requires-Dist: seaborn>=0.11.1
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+ Requires-Dist: seaborn>=0.12
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  Requires-Dist: scipy>=1.12
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  Requires-Dist: pySAM<0.20,>=0.18.1
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  Requires-Dist: Biopython>=1.79
{gwaslab-3.4.36 → gwaslab-3.4.38}/pyproject.toml RENAMED
@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "gwaslab"
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- version = "3.4.36"
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+ version = "3.4.38"
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  authors = [
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  { name="Yunye", email="yunye@gwaslab.com" },
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  ]
@@ -19,7 +19,7 @@ dependencies = [
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  "pandas>=1.3,!=1.5",
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  "numpy>=1.21.2",
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  "matplotlib>=3.5,!=3.7.2",
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- "seaborn>=0.11.1",
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+ "seaborn>=0.12",
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  "scipy>=1.12",
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  "pySAM>=0.18.1,<0.20",
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  "Biopython>=1.79",
@@ -30,7 +30,7 @@ dependencies = [
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  "gtfparse==1.3.0"
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  ]
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- requires-python = ">=3.8,<=3.10"
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+ requires-python = ">=3.9,<=3.10"
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  classifiers = [
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  "Programming Language :: Python :: 3",
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  "License :: OSI Approved :: MIT License",
{gwaslab-3.4.36 → gwaslab-3.4.38}/src/gwaslab/__init__.py RENAMED
@@ -42,6 +42,6 @@ from gwaslab.util_in_calculate_power import get_power
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  from gwaslab.util_in_calculate_power import get_beta
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  from gwaslab.viz_plot_trumpetplot import plot_power
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  from gwaslab.viz_plot_trumpetplot import plot_power_x
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- from gwaslab.util_ex_process_h5 import process_ref_vcf
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+ from gwaslab.util_ex_process_h5 import process_vcf_to_hfd5
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  from gwaslab.util_ex_run_susie import _run_susie_rss as run_susie_rss
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  from gwaslab.io_read_tabular import _read_tabular as read_tabular