gwaslab 3.6.0__tar.gz → 3.6.1__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.

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Files changed (124) hide show
  1. {gwaslab-3.6.0/src/gwaslab.egg-info → gwaslab-3.6.1}/PKG-INFO +2 -1
  2. {gwaslab-3.6.0 → gwaslab-3.6.1}/pyproject.toml +3 -2
  3. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_version.py +2 -2
  4. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_meta.py +0 -1
  5. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_meta_polars.py +0 -2
  6. {gwaslab-3.6.0 → gwaslab-3.6.1/src/gwaslab.egg-info}/PKG-INFO +2 -1
  7. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab.egg-info/requires.txt +1 -0
  8. {gwaslab-3.6.0 → gwaslab-3.6.1}/LICENSE +0 -0
  9. {gwaslab-3.6.0 → gwaslab-3.6.1}/LICENSE_before_v3.4.39 +0 -0
  10. {gwaslab-3.6.0 → gwaslab-3.6.1}/README.md +0 -0
  11. {gwaslab-3.6.0 → gwaslab-3.6.1}/setup.cfg +0 -0
  12. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/__init__.py +0 -0
  13. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/bd_common_data.py +0 -0
  14. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/bd_config.py +0 -0
  15. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/bd_download.py +0 -0
  16. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/bd_get_hapmap3.py +0 -0
  17. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/cache_manager.py +0 -0
  18. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/data/chrx_par/chrx_par_hg19.bed.gz +0 -0
  19. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/data/chrx_par/chrx_par_hg38.bed.gz +0 -0
  20. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/data/formatbook.json +0 -0
  21. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz +0 -0
  22. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz +0 -0
  23. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz +0 -0
  24. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz +0 -0
  25. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/data/reference.json +0 -0
  26. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_Log.py +0 -0
  27. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_Phenotypes.py +0 -0
  28. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_Sumstats.py +0 -0
  29. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_SumstatsMulti.py +0 -0
  30. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_SumstatsPair.py +0 -0
  31. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_SumstatsSet.py +0 -0
  32. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_SumstatsT.py +0 -0
  33. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_Sumstats_polars.py +0 -0
  34. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_Sumstats_summary.py +0 -0
  35. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_headers.py +0 -0
  36. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_meta.py +0 -0
  37. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_meta_update.py +0 -0
  38. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_vchange_status.py +0 -0
  39. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_vchange_status_polars.py +0 -0
  40. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/hm_casting.py +0 -0
  41. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/hm_casting_polars.py +0 -0
  42. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/hm_harmonize_sumstats.py +0 -0
  43. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/hm_rsid_to_chrpos.py +0 -0
  44. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/io_load_ld.py +0 -0
  45. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/io_preformat_input.py +0 -0
  46. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/io_preformat_input_polars.py +0 -0
  47. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/io_process_args.py +0 -0
  48. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/io_read_ldsc.py +0 -0
  49. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/io_read_pipcs.py +0 -0
  50. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/io_read_tabular.py +0 -0
  51. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/io_to_formats.py +0 -0
  52. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/io_to_pickle.py +0 -0
  53. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/ldsc_irwls.py +0 -0
  54. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/ldsc_jackknife.py +0 -0
  55. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/ldsc_ldscore.py +0 -0
  56. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/ldsc_parse.py +0 -0
  57. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/ldsc_regressions.py +0 -0
  58. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/ldsc_sumstats.py +0 -0
  59. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/prscs_gigrnd.py +0 -0
  60. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/prscs_mcmc_gtb.py +0 -0
  61. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/prscs_parse_genet.py +0 -0
  62. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/qc_build.py +0 -0
  63. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/qc_check_datatype.py +0 -0
  64. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/qc_check_datatype_polars.py +0 -0
  65. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/qc_fix_sumstats.py +0 -0
  66. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/qc_fix_sumstats_polars.py +0 -0
  67. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/run_script.py +0 -0
  68. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_abf_finemapping.py +0 -0
  69. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_calculate_ldmatrix.py +0 -0
  70. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_calculate_prs.py +0 -0
  71. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_gwascatalog.py +0 -0
  72. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_infer_ancestry.py +0 -0
  73. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_ldproxyfinder.py +0 -0
  74. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_ldsc.py +0 -0
  75. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_match_ldmatrix.py +0 -0
  76. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_plink_filter.py +0 -0
  77. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_process_h5.py +0 -0
  78. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_process_ref.py +0 -0
  79. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_2samplemr.py +0 -0
  80. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_ccgwas.py +0 -0
  81. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_clumping.py +0 -0
  82. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_coloc.py +0 -0
  83. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_hyprcoloc.py +0 -0
  84. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_magma.py +0 -0
  85. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_mesusie.py +0 -0
  86. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_mtag.py +0 -0
  87. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_prscs.py +0 -0
  88. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_ex_run_susie.py +0 -0
  89. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_calculate_gc.py +0 -0
  90. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_calculate_power.py +0 -0
  91. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_convert_h2.py +0 -0
  92. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_correct_winnerscurse.py +0 -0
  93. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_estimate_ess.py +0 -0
  94. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_fill_data.py +0 -0
  95. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_filter_value.py +0 -0
  96. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_get_density.py +0 -0
  97. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_get_sig.py +0 -0
  98. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_merge.py +0 -0
  99. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_snphwe.py +0 -0
  100. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_aux_annotate_plot.py +0 -0
  101. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_aux_chromatin.py +0 -0
  102. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_aux_property.py +0 -0
  103. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_aux_quickfix.py +0 -0
  104. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_aux_reposition_text.py +0 -0
  105. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_aux_save_figure.py +0 -0
  106. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_compare_af.py +0 -0
  107. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_compare_effect.py +0 -0
  108. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_credible_sets.py +0 -0
  109. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_effect.py +0 -0
  110. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_forestplot.py +0 -0
  111. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_miamiplot.py +0 -0
  112. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_miamiplot2.py +0 -0
  113. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_mqqplot.py +0 -0
  114. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_phe_heatmap.py +0 -0
  115. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_qqplot.py +0 -0
  116. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_regional2.py +0 -0
  117. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_regionalplot.py +0 -0
  118. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_rg_heatmap.py +0 -0
  119. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_scatter_with_reg.py +0 -0
  120. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_stackedregional.py +0 -0
  121. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/viz_plot_trumpetplot.py +0 -0
  122. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab.egg-info/SOURCES.txt +0 -0
  123. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab.egg-info/dependency_links.txt +0 -0
  124. {gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab.egg-info/top_level.txt +0 -0
{gwaslab-3.6.0/src/gwaslab.egg-info → gwaslab-3.6.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: gwaslab
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- Version: 3.6.0
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+ Version: 3.6.1
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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/
@@ -25,6 +25,7 @@ Requires-Dist: scikit-allel>=1.3.5
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  Requires-Dist: pyensembl==2.2.3
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  Requires-Dist: gtfparse==1.3.0
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  Requires-Dist: h5py>=3.10.0
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+ Requires-Dist: pyarrow
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  Dynamic: license-file
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  # GWASLab
{gwaslab-3.6.0 → gwaslab-3.6.1}/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 = "3.6.0"
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+ version = "3.6.1"
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  authors = [
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  { name="Yunye", email="yunye@gwaslab.com" },
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  ]
@@ -28,7 +28,8 @@ dependencies = [
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  "scikit-allel>=1.3.5",
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  "pyensembl==2.2.3",
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  "gtfparse==1.3.0",
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- "h5py>=3.10.0"
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+ "h5py>=3.10.0",
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+ "pyarrow"
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  ]
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  requires-python = ">=3.9,<3.13"
{gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_version.py RENAMED
@@ -15,8 +15,8 @@ def _get_version():
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  def gwaslab_info():
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  # version meta information
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  dic={
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- "version":"3.6.0",
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- "release_date":"20250504"
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+ "version":"3.6.1",
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+ "release_date":"20250506"
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  }
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  return dic
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{gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_meta.py RENAMED
@@ -7,7 +7,6 @@ from gwaslab.g_Log import Log
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  from gwaslab.io_to_pickle import load_data_from_pickle
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  from gwaslab.g_Sumstats import Sumstats
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  import gc
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- import statsmodels.api as sm
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  def meta_analyze(sumstats_list,
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  random_effects=False,
{gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/util_in_meta_polars.py RENAMED
@@ -6,9 +6,7 @@ from scipy.stats import norm
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  from gwaslab.g_Log import Log
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  from gwaslab.io_to_pickle import load_data_from_pickle
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  from gwaslab.g_Sumstats import Sumstats
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- import gc
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  import polars as pl
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- import statsmodels.api as sm
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  ########################################################################################################################################################################################################################################################################################################################################################
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  ########################################################################################################################################################################################################################################################################################################################################################
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  ########################################################################################################################################################################################################################################################################################################################################################
{gwaslab-3.6.0 → gwaslab-3.6.1/src/gwaslab.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: gwaslab
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- Version: 3.6.0
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+ Version: 3.6.1
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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/
@@ -25,6 +25,7 @@ Requires-Dist: scikit-allel>=1.3.5
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  Requires-Dist: pyensembl==2.2.3
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  Requires-Dist: gtfparse==1.3.0
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  Requires-Dist: h5py>=3.10.0
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+ Requires-Dist: pyarrow
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  Dynamic: license-file
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  # GWASLab
{gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab.egg-info/requires.txt RENAMED
@@ -11,3 +11,4 @@ scikit-allel>=1.3.5
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  pyensembl==2.2.3
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  gtfparse==1.3.0
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  h5py>=3.10.0
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+ pyarrow
{gwaslab-3.6.0 → gwaslab-3.6.1}/LICENSE RENAMED
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{gwaslab-3.6.0 → gwaslab-3.6.1}/LICENSE_before_v3.4.39 RENAMED
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{gwaslab-3.6.0 → gwaslab-3.6.1}/README.md RENAMED
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{gwaslab-3.6.0 → gwaslab-3.6.1}/setup.cfg RENAMED
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{gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/__init__.py RENAMED
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{gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_Log.py RENAMED
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{gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/g_meta.py RENAMED
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{gwaslab-3.6.0 → gwaslab-3.6.1}/src/gwaslab/qc_build.py RENAMED
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