gwaslab 3.4.37__py3-none-any.whl → 3.4.38__py3-none-any.whl

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Files changed (37) hide show
  1. gwaslab/data/formatbook.json +722 -721
  2. gwaslab/g_Log.py +8 -0
  3. gwaslab/g_Sumstats.py +26 -147
  4. gwaslab/g_SumstatsPair.py +6 -2
  5. gwaslab/g_Sumstats_summary.py +3 -3
  6. gwaslab/g_version.py +2 -2
  7. gwaslab/hm_casting.py +29 -15
  8. gwaslab/hm_harmonize_sumstats.py +291 -163
  9. gwaslab/hm_rsid_to_chrpos.py +1 -1
  10. gwaslab/io_preformat_input.py +43 -37
  11. gwaslab/io_to_formats.py +428 -295
  12. gwaslab/qc_check_datatype.py +3 -3
  13. gwaslab/qc_fix_sumstats.py +793 -682
  14. gwaslab/util_ex_calculate_ldmatrix.py +29 -11
  15. gwaslab/util_ex_gwascatalog.py +1 -1
  16. gwaslab/util_ex_ldproxyfinder.py +1 -1
  17. gwaslab/util_ex_process_ref.py +3 -3
  18. gwaslab/util_ex_run_coloc.py +26 -4
  19. gwaslab/util_in_convert_h2.py +1 -1
  20. gwaslab/util_in_fill_data.py +2 -2
  21. gwaslab/util_in_filter_value.py +122 -34
  22. gwaslab/util_in_get_density.py +2 -2
  23. gwaslab/util_in_get_sig.py +41 -9
  24. gwaslab/viz_aux_quickfix.py +24 -19
  25. gwaslab/viz_aux_reposition_text.py +7 -4
  26. gwaslab/viz_aux_save_figure.py +6 -5
  27. gwaslab/viz_plot_compare_af.py +5 -5
  28. gwaslab/viz_plot_miamiplot2.py +28 -20
  29. gwaslab/viz_plot_mqqplot.py +109 -72
  30. gwaslab/viz_plot_qqplot.py +11 -8
  31. gwaslab/viz_plot_regionalplot.py +3 -1
  32. gwaslab/viz_plot_trumpetplot.py +15 -6
  33. {gwaslab-3.4.37.dist-info → gwaslab-3.4.38.dist-info}/METADATA +2 -2
  34. {gwaslab-3.4.37.dist-info → gwaslab-3.4.38.dist-info}/RECORD +37 -37
  35. {gwaslab-3.4.37.dist-info → gwaslab-3.4.38.dist-info}/LICENSE +0 -0
  36. {gwaslab-3.4.37.dist-info → gwaslab-3.4.38.dist-info}/WHEEL +0 -0
  37. {gwaslab-3.4.37.dist-info → gwaslab-3.4.38.dist-info}/top_level.txt +0 -0
gwaslab/qc_check_datatype.py CHANGED
@@ -33,7 +33,7 @@ def check_datatype(sumstats, verbose=True, log=Log()):
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  log.write(" -Verified:", " ".join(verified), verbose=verbose)
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  if len(raw_verified)>0:
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- log.write(" -WARNING! Columns with possibly incompatable dtypes: {}".format(",".join(raw_verified)), verbose=verbose)
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+ log.warning("Columns with possibly incompatable dtypes: {}".format(",".join(raw_verified)), verbose=verbose)
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  except:
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  pass
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@@ -93,11 +93,11 @@ def check_dataframe_shape(sumstats, log, verbose):
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  try:
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  log.write(" -Current Dataframe shape : {} x {} ; Memory usage: {:.2f} MB".format(len(sumstats),len(sumstats.columns),memory_in_mb), verbose=verbose)
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  except:
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- log.write(" -WARNING! Error: cannot get Dataframe shape...", verbose=verbose)
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+ log.warning("Error: cannot get Dataframe shape...")
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  def check_dataframe_memory_usage(sumstats, log, verbose):
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  memory_in_mb = sumstats.memory_usage().sum()/1024/1024
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  try:
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  log.write(" -Current Dataframe memory usage: {:.2f} MB".format(memory_in_mb), verbose=verbose)
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  except:
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- log.write(" -WARNING! Error: cannot get Memory usage...", verbose=verbose)
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+ log.warning("Error: cannot get Memory usage...")