gwaslab 3.4.36__py3-none-any.whl → 3.4.38__py3-none-any.whl

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Files changed (42) hide show
  1. gwaslab/__init__.py +1 -1
  2. gwaslab/data/formatbook.json +722 -721
  3. gwaslab/g_Log.py +8 -0
  4. gwaslab/g_Sumstats.py +80 -178
  5. gwaslab/g_SumstatsPair.py +6 -2
  6. gwaslab/g_Sumstats_summary.py +3 -3
  7. gwaslab/g_meta.py +13 -3
  8. gwaslab/g_version.py +2 -2
  9. gwaslab/hm_casting.py +29 -15
  10. gwaslab/hm_harmonize_sumstats.py +312 -159
  11. gwaslab/hm_rsid_to_chrpos.py +1 -1
  12. gwaslab/io_preformat_input.py +46 -37
  13. gwaslab/io_to_formats.py +428 -295
  14. gwaslab/qc_check_datatype.py +15 -1
  15. gwaslab/qc_fix_sumstats.py +956 -719
  16. gwaslab/util_ex_calculate_ldmatrix.py +29 -11
  17. gwaslab/util_ex_gwascatalog.py +1 -1
  18. gwaslab/util_ex_ldproxyfinder.py +1 -1
  19. gwaslab/util_ex_process_h5.py +26 -17
  20. gwaslab/util_ex_process_ref.py +3 -3
  21. gwaslab/util_ex_run_coloc.py +26 -4
  22. gwaslab/util_in_convert_h2.py +1 -1
  23. gwaslab/util_in_fill_data.py +44 -5
  24. gwaslab/util_in_filter_value.py +122 -34
  25. gwaslab/util_in_get_density.py +2 -2
  26. gwaslab/util_in_get_sig.py +41 -9
  27. gwaslab/viz_aux_quickfix.py +26 -21
  28. gwaslab/viz_aux_reposition_text.py +7 -4
  29. gwaslab/viz_aux_save_figure.py +6 -5
  30. gwaslab/viz_plot_compare_af.py +5 -5
  31. gwaslab/viz_plot_compare_effect.py +22 -5
  32. gwaslab/viz_plot_miamiplot2.py +28 -20
  33. gwaslab/viz_plot_mqqplot.py +214 -98
  34. gwaslab/viz_plot_qqplot.py +11 -8
  35. gwaslab/viz_plot_regionalplot.py +16 -9
  36. gwaslab/viz_plot_trumpetplot.py +15 -6
  37. {gwaslab-3.4.36.dist-info → gwaslab-3.4.38.dist-info}/METADATA +3 -3
  38. gwaslab-3.4.38.dist-info/RECORD +72 -0
  39. gwaslab-3.4.36.dist-info/RECORD +0 -72
  40. {gwaslab-3.4.36.dist-info → gwaslab-3.4.38.dist-info}/LICENSE +0 -0
  41. {gwaslab-3.4.36.dist-info → gwaslab-3.4.38.dist-info}/WHEEL +0 -0
  42. {gwaslab-3.4.36.dist-info → gwaslab-3.4.38.dist-info}/top_level.txt +0 -0
gwaslab/__init__.py CHANGED
@@ -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