gwaslab 3.6.6__py3-none-any.whl → 3.6.8__py3-none-any.whl

gwaslab/g_SumstatsSet.py

@@ -3,91 +3,98 @@ import numpy as np
 import time
 import re
 import copy
-from gwaslab.g_Sumstats_summary import summarize
-from gwaslab.g_Sumstats_summary import lookupstatus
-from gwaslab.io_preformat_input import preformat
-from gwaslab.io_to_formats import _to_format
-from gwaslab.g_Log import Log
-from gwaslab.qc_fix_sumstats import fixID
-from gwaslab.qc_fix_sumstats import flipSNPID
-from gwaslab.qc_fix_sumstats import stripSNPID
-from gwaslab.qc_fix_sumstats import removedup
-from gwaslab.qc_fix_sumstats import fixchr
-from gwaslab.qc_fix_sumstats import fixpos
-from gwaslab.qc_fix_sumstats import fixallele
-from gwaslab.qc_fix_sumstats import parallelnormalizeallele
-from gwaslab.qc_fix_sumstats import sanitycheckstats
-from gwaslab.qc_fix_sumstats import parallelizeliftovervariant
-from gwaslab.qc_fix_sumstats import flipallelestats
-from gwaslab.qc_fix_sumstats import sortcoordinate
-from gwaslab.qc_fix_sumstats import sortcolumn
-from gwaslab.qc_fix_sumstats import _set_build
-from gwaslab.qc_fix_sumstats import _process_build
-from gwaslab.hm_harmonize_sumstats import parallelecheckaf
-from gwaslab.hm_harmonize_sumstats import paralleleinferaf
-from gwaslab.hm_harmonize_sumstats import checkref
-from gwaslab.hm_harmonize_sumstats import oldcheckref
-from gwaslab.hm_harmonize_sumstats import rsidtochrpos
-from gwaslab.hm_harmonize_sumstats import parallelizeassignrsid
-from gwaslab.hm_harmonize_sumstats import parallelinferstrand
-from gwaslab.hm_harmonize_sumstats import parallelrsidtochrpos
-from gwaslab.hm_harmonize_sumstats import _paralleleinferafwithmaf
-from gwaslab.util_in_filter_value import filtervalues
-from gwaslab.util_in_filter_value import filterout
-from gwaslab.util_in_filter_value import filterin
-from gwaslab.util_in_filter_value import filterregionin
-from gwaslab.util_in_filter_value import filterregionout
-from gwaslab.util_in_filter_value import _filter_indel
-from gwaslab.util_in_filter_value import _filter_palindromic
-from gwaslab.util_in_filter_value import _filter_snp
-from gwaslab.util_in_filter_value import _exclude_hla
-from gwaslab.util_in_filter_value import inferbuild
-from gwaslab.util_in_filter_value import sampling
-from gwaslab.util_in_filter_value import _get_flanking
-from gwaslab.util_in_filter_value import _get_flanking_by_chrpos
-from gwaslab.util_in_filter_value import _get_flanking_by_id
-from gwaslab.util_in_calculate_gc import lambdaGC
-from gwaslab.util_in_convert_h2 import _get_per_snp_r2
-from gwaslab.util_in_get_sig import getsig
-from gwaslab.util_in_get_density import getsignaldensity
-from gwaslab.util_in_get_density import assigndensity
-from gwaslab.util_in_get_sig import annogene
-from gwaslab.util_in_get_sig import getnovel
-from gwaslab.util_in_get_sig import _check_cis
-from gwaslab.util_in_get_sig import _check_novel_set
-from gwaslab.util_in_fill_data import filldata
-from gwaslab.bd_get_hapmap3 import gethapmap3
-from gwaslab.bd_common_data import get_chr_list
-from gwaslab.bd_common_data import get_number_to_chr
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_high_ld
-from gwaslab.bd_common_data import get_format_dict
-from gwaslab.bd_common_data import get_formats_list
+import gc
+
 from gwaslab.g_version import _show_version
 from gwaslab.g_version import gwaslab_info
 from gwaslab.g_meta import _init_meta
 from gwaslab.g_meta import _append_meta_record
-from gwaslab.util_ex_run_clumping import _clump
-from gwaslab.util_ex_calculate_ldmatrix import tofinemapping
-from gwaslab.util_ex_calculate_prs import _calculate_prs
-from gwaslab.viz_plot_mqqplot import mqqplot
-from gwaslab.viz_plot_trumpetplot import plottrumpet
-from gwaslab.viz_plot_compare_af import plotdaf
-from gwaslab.util_ex_run_susie import _run_susie_rss
-from gwaslab.qc_fix_sumstats import _check_data_consistency
-from gwaslab.util_ex_ldsc import _estimate_h2_by_ldsc
-from gwaslab.util_ex_ldsc import _estimate_rg_by_ldsc
-from gwaslab.util_ex_ldsc import _estimate_h2_cts_by_ldsc
-from gwaslab.util_ex_ldsc import _estimate_partitioned_h2_by_ldsc 
-from gwaslab.bd_get_hapmap3 import gethapmap3
-from gwaslab.util_abf_finemapping import abf_finemapping
-from gwaslab.util_abf_finemapping import make_cs
-from gwaslab.io_read_pipcs import _read_pipcs
-from gwaslab.viz_plot_credible_sets import _plot_cs
-import gc
-from gwaslab.viz_plot_phe_heatmap import _gwheatmap
-from gwaslab.viz_plot_effect import _plot_effect
-from gwaslab.util_in_merge import _extract_variant
+from gwaslab.g_Sumstats_summary import summarize
+from gwaslab.g_Sumstats_summary import lookupstatus
+from gwaslab.g_Log import Log
+
+from gwaslab.qc.qc_fix_sumstats import fixID
+from gwaslab.qc.qc_fix_sumstats import flipSNPID
+from gwaslab.qc.qc_fix_sumstats import stripSNPID
+from gwaslab.qc.qc_fix_sumstats import removedup
+from gwaslab.qc.qc_fix_sumstats import fixchr
+from gwaslab.qc.qc_fix_sumstats import fixpos
+from gwaslab.qc.qc_fix_sumstats import fixallele
+from gwaslab.qc.qc_fix_sumstats import parallelnormalizeallele
+from gwaslab.qc.qc_fix_sumstats import sanitycheckstats
+from gwaslab.qc.qc_fix_sumstats import parallelizeliftovervariant
+from gwaslab.qc.qc_fix_sumstats import flipallelestats
+from gwaslab.qc.qc_fix_sumstats import sortcoordinate
+from gwaslab.qc.qc_fix_sumstats import sortcolumn
+from gwaslab.qc.qc_fix_sumstats import _set_build
+from gwaslab.qc.qc_fix_sumstats import _process_build
+from gwaslab.qc.qc_fix_sumstats import _check_data_consistency
+
+from gwaslab.hm.hm_harmonize_sumstats import parallelecheckaf
+from gwaslab.hm.hm_harmonize_sumstats import paralleleinferaf
+from gwaslab.hm.hm_harmonize_sumstats import checkref
+from gwaslab.hm.hm_harmonize_sumstats import oldcheckref
+from gwaslab.hm.hm_harmonize_sumstats import rsidtochrpos
+from gwaslab.hm.hm_harmonize_sumstats import parallelizeassignrsid
+from gwaslab.hm.hm_harmonize_sumstats import parallelinferstrand
+from gwaslab.hm.hm_harmonize_sumstats import parallelrsidtochrpos
+from gwaslab.hm.hm_harmonize_sumstats import _paralleleinferafwithmaf
+
+from gwaslab.util.util_in_filter_value import filtervalues
+from gwaslab.util.util_in_filter_value import filterout
+from gwaslab.util.util_in_filter_value import filterin
+from gwaslab.util.util_in_filter_value import filterregionin
+from gwaslab.util.util_in_filter_value import filterregionout
+from gwaslab.util.util_in_filter_value import _filter_indel
+from gwaslab.util.util_in_filter_value import _filter_palindromic
+from gwaslab.util.util_in_filter_value import _filter_snp
+from gwaslab.util.util_in_filter_value import _exclude_hla
+from gwaslab.util.util_in_filter_value import inferbuild
+from gwaslab.util.util_in_filter_value import sampling
+from gwaslab.util.util_in_filter_value import _get_flanking
+from gwaslab.util.util_in_filter_value import _get_flanking_by_chrpos
+from gwaslab.util.util_in_filter_value import _get_flanking_by_id
+from gwaslab.util.util_in_calculate_gc import lambdaGC
+from gwaslab.util.util_in_convert_h2 import _get_per_snp_r2
+from gwaslab.util.util_in_get_sig import getsig
+from gwaslab.util.util_in_get_density import getsignaldensity
+from gwaslab.util.util_in_get_density import assigndensity
+from gwaslab.util.util_in_get_sig import annogene
+from gwaslab.util.util_in_get_sig import getnovel
+from gwaslab.util.util_in_get_sig import _check_cis
+from gwaslab.util.util_in_get_sig import _check_novel_set
+from gwaslab.util.util_in_fill_data import filldata
+from gwaslab.util.util_ex_run_clumping import _clump
+from gwaslab.util.util_ex_calculate_ldmatrix import tofinemapping
+from gwaslab.util.util_ex_calculate_prs import _calculate_prs
+from gwaslab.util.util_ex_ldsc import _estimate_h2_by_ldsc
+from gwaslab.util.util_ex_ldsc import _estimate_rg_by_ldsc
+from gwaslab.util.util_ex_ldsc import _estimate_h2_cts_by_ldsc
+from gwaslab.util.util_ex_ldsc import _estimate_partitioned_h2_by_ldsc 
+from gwaslab.util.util_abf_finemapping import abf_finemapping
+from gwaslab.util.util_abf_finemapping import make_cs
+from gwaslab.util.util_in_merge import _extract_variant
+from gwaslab.util.util_ex_run_susie import _run_susie_rss
+
+from gwaslab.bd.bd_get_hapmap3 import gethapmap3
+from gwaslab.bd.bd_common_data import get_chr_list
+from gwaslab.bd.bd_common_data import get_number_to_chr
+from gwaslab.bd.bd_common_data import get_chr_to_number
+from gwaslab.bd.bd_common_data import get_high_ld
+from gwaslab.bd.bd_common_data import get_format_dict
+from gwaslab.bd.bd_common_data import get_formats_list
+from gwaslab.bd.bd_get_hapmap3 import gethapmap3
+
+from gwaslab.viz.viz_plot_mqqplot import mqqplot
+from gwaslab.viz.viz_plot_trumpetplot import plottrumpet
+from gwaslab.viz.viz_plot_compare_af import plotdaf
+from gwaslab.viz.viz_plot_credible_sets import _plot_cs
+from gwaslab.viz.viz_plot_phe_heatmap import _gwheatmap
+from gwaslab.viz.viz_plot_effect import _plot_effect
+
+from gwaslab.io.io_read_pipcs import _read_pipcs
+from gwaslab.io.io_preformat_input import preformat
+from gwaslab.io.io_to_formats import _to_format
 
 #20250215
 class SumstatsSet():

gwaslab/g_SumstatsT.py

@@ -1,13 +1,13 @@
 import pandas as pd
 import numpy as np
 from gwaslab.g_Sumstats import Sumstats
-from gwaslab.hm_casting import _merge_mold_with_sumstats_by_chrpos
-from gwaslab.hm_casting import _align_with_mold
-from gwaslab.hm_casting import _fill_missing_columns
-from gwaslab.hm_casting import _check_daf
+from gwaslab.hm.hm_casting import _merge_mold_with_sumstats_by_chrpos
+from gwaslab.hm.hm_casting import _align_with_mold
+from gwaslab.hm.hm_casting import _fill_missing_columns
+from gwaslab.hm.hm_casting import _check_daf
+from gwaslab.hm.hm_casting import _assign_warning_code
 
-from gwaslab.hm_casting import _assign_warning_code
-from gwaslab.qc_fix_sumstats import flipallelestats
+from gwaslab.qc.qc_fix_sumstats import flipallelestats
 
 
 class SumstatsT( ):

gwaslab/g_Sumstats_polars.py

@@ -4,97 +4,97 @@ import time
 import copy
 from gwaslab.g_Sumstats_summary import summarize
 from gwaslab.g_Sumstats_summary import lookupstatus
-from gwaslab.io_preformat_input_polars import preformatp
-from gwaslab.io_to_formats import _to_format
+from gwaslab.io.io_preformat_input_polars import preformatp
+from gwaslab.io.io_to_formats import _to_format
 from gwaslab.g_Log import Log
-from gwaslab.qc_fix_sumstats import fixID
-from gwaslab.qc_fix_sumstats import flipSNPID
-from gwaslab.qc_fix_sumstats import stripSNPID
-from gwaslab.qc_fix_sumstats import removedup
-from gwaslab.qc_fix_sumstats import fixchr
-from gwaslab.qc_fix_sumstats import fixpos
-from gwaslab.qc_fix_sumstats import fixallele
-from gwaslab.qc_fix_sumstats import parallelnormalizeallele
-from gwaslab.qc_fix_sumstats import sanitycheckstats
-from gwaslab.qc_fix_sumstats import parallelizeliftovervariant
-from gwaslab.qc_fix_sumstats import flipallelestats
-from gwaslab.qc_fix_sumstats import sortcoordinate
-from gwaslab.qc_fix_sumstats import sortcolumn
-from gwaslab.qc_fix_sumstats import _set_build
-from gwaslab.qc_fix_sumstats import _process_build
-from gwaslab.hm_harmonize_sumstats import parallelecheckaf
-from gwaslab.hm_harmonize_sumstats import paralleleinferaf
-from gwaslab.hm_harmonize_sumstats import checkref
-from gwaslab.hm_harmonize_sumstats import oldcheckref
-from gwaslab.hm_harmonize_sumstats import rsidtochrpos
-from gwaslab.hm_harmonize_sumstats import parallelizeassignrsid
-from gwaslab.hm_harmonize_sumstats import parallelinferstrand
-from gwaslab.hm_harmonize_sumstats import parallelrsidtochrpos
-from gwaslab.hm_harmonize_sumstats import _paralleleinferafwithmaf
-from gwaslab.util_in_filter_value import filtervalues
-from gwaslab.util_in_filter_value import filterout
-from gwaslab.util_in_filter_value import filterin
-from gwaslab.util_in_filter_value import filterregionin
-from gwaslab.util_in_filter_value import filterregionout
-from gwaslab.util_in_filter_value import _filter_indel
-from gwaslab.util_in_filter_value import _filter_palindromic
-from gwaslab.util_in_filter_value import _filter_snp
-from gwaslab.util_in_filter_value import _filter_region
-from gwaslab.util_in_filter_value import _exclude_hla
-from gwaslab.util_in_filter_value import _search_variants
-from gwaslab.util_in_filter_value import inferbuild
-from gwaslab.util_in_filter_value import sampling
-from gwaslab.util_in_filter_value import _get_flanking
-from gwaslab.util_in_filter_value import _get_flanking_by_chrpos
-from gwaslab.util_in_filter_value import _get_flanking_by_id
-from gwaslab.util_in_calculate_gc import lambdaGC
-from gwaslab.util_in_convert_h2 import _get_per_snp_r2
-from gwaslab.util_in_get_sig import getsig
-from gwaslab.util_in_get_density import getsignaldensity
-from gwaslab.util_in_get_density import assigndensity
-from gwaslab.util_in_get_sig import annogene
-from gwaslab.util_in_get_sig import getnovel
-from gwaslab.util_in_get_sig import _check_cis
-from gwaslab.util_in_get_sig import _check_novel_set
-from gwaslab.util_in_fill_data import filldata
-from gwaslab.bd_get_hapmap3 import gethapmap3
-from gwaslab.bd_common_data import get_chr_list
-from gwaslab.bd_common_data import get_number_to_chr
-from gwaslab.bd_common_data import get_chr_to_number
-from gwaslab.bd_common_data import get_high_ld
-from gwaslab.bd_common_data import get_format_dict
-from gwaslab.bd_common_data import get_formats_list
+from gwaslab.qc.qc_fix_sumstats import fixID
+from gwaslab.qc.qc_fix_sumstats import flipSNPID
+from gwaslab.qc.qc_fix_sumstats import stripSNPID
+from gwaslab.qc.qc_fix_sumstats import removedup
+from gwaslab.qc.qc_fix_sumstats import fixchr
+from gwaslab.qc.qc_fix_sumstats import fixpos
+from gwaslab.qc.qc_fix_sumstats import fixallele
+from gwaslab.qc.qc_fix_sumstats import parallelnormalizeallele
+from gwaslab.qc.qc_fix_sumstats import sanitycheckstats
+from gwaslab.qc.qc_fix_sumstats import parallelizeliftovervariant
+from gwaslab.qc.qc_fix_sumstats import flipallelestats
+from gwaslab.qc.qc_fix_sumstats import sortcoordinate
+from gwaslab.qc.qc_fix_sumstats import sortcolumn
+from gwaslab.qc.qc_fix_sumstats import _set_build
+from gwaslab.qc.qc_fix_sumstats import _process_build
+from gwaslab.hm.hm_harmonize_sumstats import parallelecheckaf
+from gwaslab.hm.hm_harmonize_sumstats import paralleleinferaf
+from gwaslab.hm.hm_harmonize_sumstats import checkref
+from gwaslab.hm.hm_harmonize_sumstats import oldcheckref
+from gwaslab.hm.hm_harmonize_sumstats import rsidtochrpos
+from gwaslab.hm.hm_harmonize_sumstats import parallelizeassignrsid
+from gwaslab.hm.hm_harmonize_sumstats import parallelinferstrand
+from gwaslab.hm.hm_harmonize_sumstats import parallelrsidtochrpos
+from gwaslab.hm.hm_harmonize_sumstats import _paralleleinferafwithmaf
+from gwaslab.util.util_in_filter_value import filtervalues
+from gwaslab.util.util_in_filter_value import filterout
+from gwaslab.util.util_in_filter_value import filterin
+from gwaslab.util.util_in_filter_value import filterregionin
+from gwaslab.util.util_in_filter_value import filterregionout
+from gwaslab.util.util_in_filter_value import _filter_indel
+from gwaslab.util.util_in_filter_value import _filter_palindromic
+from gwaslab.util.util_in_filter_value import _filter_snp
+from gwaslab.util.util_in_filter_value import _filter_region
+from gwaslab.util.util_in_filter_value import _exclude_hla
+from gwaslab.util.util_in_filter_value import _search_variants
+from gwaslab.util.util_in_filter_value import inferbuild
+from gwaslab.util.util_in_filter_value import sampling
+from gwaslab.util.util_in_filter_value import _get_flanking
+from gwaslab.util.util_in_filter_value import _get_flanking_by_chrpos
+from gwaslab.util.util_in_filter_value import _get_flanking_by_id
+from gwaslab.util.util_in_calculate_gc import lambdaGC
+from gwaslab.util.util_in_convert_h2 import _get_per_snp_r2
+from gwaslab.util.util_in_get_sig import getsig
+from gwaslab.util.util_in_get_density import getsignaldensity
+from gwaslab.util.util_in_get_density import assigndensity
+from gwaslab.util.util_in_get_sig import annogene
+from gwaslab.util.util_in_get_sig import getnovel
+from gwaslab.util.util_in_get_sig import _check_cis
+from gwaslab.util.util_in_get_sig import _check_novel_set
+from gwaslab.util.util_in_fill_data import filldata
+from gwaslab.bd.bd_get_hapmap3 import gethapmap3
+from gwaslab.bd.bd_common_data import get_chr_list
+from gwaslab.bd.bd_common_data import get_number_to_chr
+from gwaslab.bd.bd_common_data import get_chr_to_number
+from gwaslab.bd.bd_common_data import get_high_ld
+from gwaslab.bd.bd_common_data import get_format_dict
+from gwaslab.bd.bd_common_data import get_formats_list
 from gwaslab.g_version import _show_version
 from gwaslab.g_version import gwaslab_info
 from gwaslab.g_meta import _init_meta
 from gwaslab.g_meta import _append_meta_record
 from gwaslab.g_meta_update import _update_meta
-from gwaslab.util_ex_run_clumping import _clump
-from gwaslab.util_ex_calculate_ldmatrix import tofinemapping
-from gwaslab.io_load_ld import tofinemapping_using_ld
-from gwaslab.util_ex_calculate_prs import _calculate_prs
-from gwaslab.viz_plot_mqqplot import mqqplot
-from gwaslab.viz_plot_trumpetplot import plottrumpet
-from gwaslab.viz_plot_compare_af import plotdaf
-from gwaslab.util_ex_run_susie import _run_susie_rss
-from gwaslab.util_ex_run_susie import _get_cs_lead
-from gwaslab.qc_fix_sumstats import _check_data_consistency
-from gwaslab.util_ex_ldsc import _estimate_h2_by_ldsc
-from gwaslab.util_ex_ldsc import _estimate_rg_by_ldsc
-from gwaslab.util_ex_ldsc import _estimate_h2_cts_by_ldsc
-from gwaslab.util_ex_ldsc import _estimate_partitioned_h2_by_ldsc 
-from gwaslab.util_ex_ldproxyfinder import _extract_ld_proxy
-from gwaslab.bd_get_hapmap3 import gethapmap3
-from gwaslab.util_abf_finemapping import abf_finemapping
-from gwaslab.util_abf_finemapping import make_cs
-from gwaslab.io_read_pipcs import _read_pipcs
-from gwaslab.util_in_estimate_ess import _get_ess
-from gwaslab.viz_plot_credible_sets import _plot_cs
-from gwaslab.hm_casting import _align_with_mold
-from gwaslab.hm_casting  import _merge_mold_with_sumstats_by_chrpos
+from gwaslab.util.util_ex_run_clumping import _clump
+from gwaslab.util.util_ex_calculate_ldmatrix import tofinemapping
+from gwaslab.io.io_load_ld import tofinemapping_using_ld
+from gwaslab.util.util_ex_calculate_prs import _calculate_prs
+from gwaslab.viz.viz_plot_mqqplot import mqqplot
+from gwaslab.viz.viz_plot_trumpetplot import plottrumpet
+from gwaslab.viz.viz_plot_compare_af import plotdaf
+from gwaslab.util.util_ex_run_susie import _run_susie_rss
+from gwaslab.util.util_ex_run_susie import _get_cs_lead
+from gwaslab.qc.qc_fix_sumstats import _check_data_consistency
+from gwaslab.util.util_ex_ldsc import _estimate_h2_by_ldsc
+from gwaslab.util.util_ex_ldsc import _estimate_rg_by_ldsc
+from gwaslab.util.util_ex_ldsc import _estimate_h2_cts_by_ldsc
+from gwaslab.util.util_ex_ldsc import _estimate_partitioned_h2_by_ldsc 
+from gwaslab.util.util_ex_ldproxyfinder import _extract_ld_proxy
+from gwaslab.bd.bd_get_hapmap3 import gethapmap3
+from gwaslab.util.util_abf_finemapping import abf_finemapping
+from gwaslab.util.util_abf_finemapping import make_cs
+from gwaslab.io.io_read_pipcs import _read_pipcs
+from gwaslab.util.util_in_estimate_ess import _get_ess
+from gwaslab.viz.viz_plot_credible_sets import _plot_cs
+from gwaslab.hm.hm_casting import _align_with_mold
+from gwaslab.hm.hm_casting  import _merge_mold_with_sumstats_by_chrpos
 import gc
-from gwaslab.viz_plot_phe_heatmap import _gwheatmap
-from gwaslab.util_ex_run_prscs import _run_prscs
+from gwaslab.viz.viz_plot_phe_heatmap import _gwheatmap
+from gwaslab.util.util_ex_run_prscs import _run_prscs
 
 #20220309
 class Sumstatsp():

gwaslab/g_meta_update.py

@@ -1,5 +1,5 @@
 import numpy as np
-from gwaslab.util_in_filter_value import inferbuild
+from gwaslab.util.util_in_filter_value import inferbuild
 from gwaslab.g_Log import Log
 import time
 

gwaslab/g_vchange_status.py

@@ -1,15 +1,15 @@
 import pandas as pd
 
-CATEGORIES = {str(j+i) for j in [1300000,1800000,1900000,3800000,9700000,9800000,9900000] for i in range(0,100000)}
+STATUS_CATEGORIES = [str(j+i) for j in [1300000,1800000,1900000,3800000,3900000,9700000,9800000,9900000] for i in range(0,100000)]
 
 def vchange_status(status,digit,before,after):
     dic={}
     for i in range(len(before)):
-        dic[before[i]]=after[i]
+        dic[str(before[i])] = str(after[i])
     if digit>1:
-        return pd.Categorical(status.str[:digit-1]+status.str[digit-1].replace(dic)+status.str[digit:],categories=CATEGORIES)
+        return pd.Categorical(status.str[:digit-1] + status.str[digit-1].replace(dic) + status.str[digit:],categories=STATUS_CATEGORIES)
     else:
-        return pd.Categorical(status.str[digit-1].replace(dic)+status.str[digit:],categories=CATEGORIES)
+        return pd.Categorical(status.str[digit-1].replace(dic) + status.str[digit:],categories=STATUS_CATEGORIES)
 
 def copy_status(from_status,to_status, digit):
     if digit>1:

gwaslab/g_version.py

@@ -17,8 +17,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.6.6",
-   "release_date":"20250704"
+   "version":"3.6.0",
+   "release_date":"20250902"
     }
     return dic   
 

gwaslab/{hm_casting.py → hm/hm_casting.py}

@@ -4,10 +4,10 @@ from gwaslab.g_Log import Log
 from pandas.api.types import CategoricalDtype
 from gwaslab.g_vchange_status import copy_status
 from gwaslab.g_vchange_status import vchange_status
-from gwaslab.qc_fix_sumstats import flipallelestats
-from gwaslab.qc_check_datatype import check_datatype
-from gwaslab.qc_fix_sumstats import start_to
-from gwaslab.util_in_fill_data import filldata
+from gwaslab.qc.qc_fix_sumstats import flipallelestats
+from gwaslab.qc.qc_check_datatype import check_datatype
+from gwaslab.qc.qc_fix_sumstats import start_to
+from gwaslab.util.util_in_fill_data import filldata
 from Bio import SeqIO
 from itertools import combinations
 

gwaslab/{hm_casting_polars.py → hm/hm_casting_polars.py}

@@ -5,10 +5,10 @@ from pandas.api.types import CategoricalDtype
 from gwaslab.g_vchange_status import copy_status
 from gwaslab.g_vchange_status_polars import vchange_statusp
 from gwaslab.g_vchange_status_polars import copy_statusp
-from gwaslab.qc_fix_sumstats import flipallelestats
-from gwaslab.qc_check_datatype import check_datatype
-from gwaslab.qc_fix_sumstats import start_to
-from gwaslab.util_in_fill_data import filldata
+from gwaslab.qc.qc_fix_sumstats import flipallelestats
+from gwaslab.qc.qc_check_datatype import check_datatype
+from gwaslab.qc.qc_fix_sumstats import start_to
+from gwaslab.util.util_in_fill_data import filldata
 from Bio import SeqIO
 from itertools import combinations
 import polars as pl