gwaslab 3.4.36__py3-none-any.whl → 3.4.38__py3-none-any.whl
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- gwaslab/__init__.py +1 -1
- gwaslab/data/formatbook.json +722 -721
- gwaslab/g_Log.py +8 -0
- gwaslab/g_Sumstats.py +80 -178
- gwaslab/g_SumstatsPair.py +6 -2
- gwaslab/g_Sumstats_summary.py +3 -3
- gwaslab/g_meta.py +13 -3
- gwaslab/g_version.py +2 -2
- gwaslab/hm_casting.py +29 -15
- gwaslab/hm_harmonize_sumstats.py +312 -159
- gwaslab/hm_rsid_to_chrpos.py +1 -1
- gwaslab/io_preformat_input.py +46 -37
- gwaslab/io_to_formats.py +428 -295
- gwaslab/qc_check_datatype.py +15 -1
- gwaslab/qc_fix_sumstats.py +956 -719
- gwaslab/util_ex_calculate_ldmatrix.py +29 -11
- gwaslab/util_ex_gwascatalog.py +1 -1
- gwaslab/util_ex_ldproxyfinder.py +1 -1
- gwaslab/util_ex_process_h5.py +26 -17
- gwaslab/util_ex_process_ref.py +3 -3
- gwaslab/util_ex_run_coloc.py +26 -4
- gwaslab/util_in_convert_h2.py +1 -1
- gwaslab/util_in_fill_data.py +44 -5
- gwaslab/util_in_filter_value.py +122 -34
- gwaslab/util_in_get_density.py +2 -2
- gwaslab/util_in_get_sig.py +41 -9
- gwaslab/viz_aux_quickfix.py +26 -21
- gwaslab/viz_aux_reposition_text.py +7 -4
- gwaslab/viz_aux_save_figure.py +6 -5
- gwaslab/viz_plot_compare_af.py +5 -5
- gwaslab/viz_plot_compare_effect.py +22 -5
- gwaslab/viz_plot_miamiplot2.py +28 -20
- gwaslab/viz_plot_mqqplot.py +214 -98
- gwaslab/viz_plot_qqplot.py +11 -8
- gwaslab/viz_plot_regionalplot.py +16 -9
- gwaslab/viz_plot_trumpetplot.py +15 -6
- {gwaslab-3.4.36.dist-info → gwaslab-3.4.38.dist-info}/METADATA +3 -3
- gwaslab-3.4.38.dist-info/RECORD +72 -0
- gwaslab-3.4.36.dist-info/RECORD +0 -72
- {gwaslab-3.4.36.dist-info → gwaslab-3.4.38.dist-info}/LICENSE +0 -0
- {gwaslab-3.4.36.dist-info → gwaslab-3.4.38.dist-info}/WHEEL +0 -0
- {gwaslab-3.4.36.dist-info → gwaslab-3.4.38.dist-info}/top_level.txt +0 -0
gwaslab/qc_check_datatype.py
CHANGED
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@@ -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.
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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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@@ -87,3 +87,17 @@ def verify_datatype(header, dtype):
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return "F"
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else:
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return "NA"
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+
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def check_dataframe_shape(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 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.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.warning("Error: cannot get Memory usage...")
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