gwaslab 3.6.2__py3-none-any.whl → 3.6.3__py3-none-any.whl

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Files changed (12) hide show
  1. gwaslab/g_Sumstats.py +1 -1
  2. gwaslab/g_version.py +4 -2
  3. gwaslab/io_load_ld.py +3 -1
  4. gwaslab/io_preformat_input.py +5 -3
  5. gwaslab/util_ex_run_clumping.py +8 -4
  6. gwaslab/util_ex_run_scdrs.py +1 -1
  7. {gwaslab-3.6.2.dist-info → gwaslab-3.6.3.dist-info}/METADATA +1 -1
  8. {gwaslab-3.6.2.dist-info → gwaslab-3.6.3.dist-info}/RECORD +12 -12
  9. {gwaslab-3.6.2.dist-info → gwaslab-3.6.3.dist-info}/WHEEL +1 -1
  10. {gwaslab-3.6.2.dist-info → gwaslab-3.6.3.dist-info}/licenses/LICENSE +0 -0
  11. {gwaslab-3.6.2.dist-info → gwaslab-3.6.3.dist-info}/licenses/LICENSE_before_v3.4.39 +0 -0
  12. {gwaslab-3.6.2.dist-info → gwaslab-3.6.3.dist-info}/top_level.txt +0 -0
gwaslab/g_Sumstats.py CHANGED
@@ -102,7 +102,7 @@ from gwaslab.util_ex_run_scdrs import _run_scdrs
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  #20220309
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  class Sumstats():
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  def __init__(self,
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- sumstats,
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+ sumstats=None,
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  fmt=None,
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  tab_fmt="tsv",
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  snpid=None,
gwaslab/g_version.py CHANGED
@@ -2,11 +2,13 @@ from gwaslab.g_Log import Log
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  import subprocess
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  import os
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  import numpy as np
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+ import sys
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  def _show_version(log=Log(), verbose=True):
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  # show version when loading sumstats
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  log.write("GWASLab v{} https://cloufield.github.io/gwaslab/".format(gwaslab_info()["version"]),verbose=verbose)
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  log.write("(C) 2022-2025, Yunye He, Kamatani Lab, GPL-3.0 license, gwaslab@gmail.com",verbose=verbose)
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+ log.write(f"Python version: {sys.version}",verbose=verbose)
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  def _get_version():
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  # return short version string like v3.4.33
@@ -15,8 +17,8 @@ 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":"3.6.2",
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- "release_date":"20250509"
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+ "version":"3.6.3",
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+ "release_date":"202505"
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  }
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  return dic
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gwaslab/io_load_ld.py CHANGED
@@ -233,7 +233,9 @@ def process_ld(sumstats,
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  lead_snpid = matched_snpid.group(0).split(":")[1:]
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  lead_snpid[0]= int(lead_snpid[0])
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  lead_series = pd.Series(lead_snpid)
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-
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+
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+ print(sumstats)
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+ print(sumstats.loc[lead_id, "REFINDEX"])
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  # if lead pos is available:
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  if sumstats.loc[lead_id, "REFINDEX"] is not None:
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  lead_snp_ref_index = sumstats.loc[lead_id, "REFINDEX"]
gwaslab/io_preformat_input.py CHANGED
@@ -58,7 +58,7 @@ def preformat(sumstats,
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  study=None,
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  trait=None,
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  build=None,
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- other=[],
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+ other=None,
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  usekeys=None,
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  chrom_pat=None,
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  snpid_pat=None,
@@ -68,8 +68,10 @@ def preformat(sumstats,
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  #renaming dictionary
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  rename_dictionary = {}
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- usecols = []
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- dtype_dictionary ={}
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+ usecols = list()
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+ if other is None:
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+ other = list()
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+ dtype_dictionary = {}
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  if readargs is None:
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  readargs={}
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  #######################################################################################################################################################
gwaslab/util_ex_run_clumping.py CHANGED
@@ -9,7 +9,7 @@ from gwaslab.util_ex_process_ref import _process_plink_input_files
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  from gwaslab.g_version import _checking_plink_version
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  def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2",
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- p="P",mlog10p="MLOG10P", overwrite=False, study=None, bfile=None,
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+ p="P",mlog10p="MLOG10P", overwrite=False, study=None, bfile=None, pfile=None,
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  n_cores=1, memory=None, chrom=None, clump_p1=5e-8, clump_p2=5e-8, clump_r2=0.01, clump_kb=250,
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  log=Log(),verbose=True,plink="plink",plink2="plink2"):
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  ##start function with col checking##########################################################
@@ -54,6 +54,7 @@ def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2",
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  # process reference file
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  bfile, plink_log, ref_bim,filetype = _process_plink_input_files(chrlist=sumstats["CHR"].unique(),
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  bfile=bfile,
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+ pfile=pfile,
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  vcf=vcf,
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  n_cores=n_cores,
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  plink_log=plink_log,
@@ -162,9 +163,12 @@ def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2",
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  log.write(e.output)
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  #os.system(script)
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- clumped = pd.read_csv("{}.clumps".format(out_single_chr),sep="\s+")
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- results = pd.concat([results,clumped],ignore_index=True)
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-
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+ try:
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+ clumped = pd.read_csv("{}.clumps".format(out_single_chr),sep="\s+")
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+ results = pd.concat([results,clumped],ignore_index=True)
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+
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+ except:
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+ log.write(f"Clumping failed for chr{i}")
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  # remove temp SNPIDP file
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  os.remove(clump)
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gwaslab/util_ex_run_scdrs.py CHANGED
@@ -84,7 +84,7 @@ def _run_scdrs( scdrs="scdrs",
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  bash_script+=f'''
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  {python} {scdrs} perform-downstream {analysis_string} \
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  --h5ad-file {h5ad_file} \
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- --score-file {trait}.full_score.gz \
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+ --score-file ./{trait}.full_score.gz \
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  --out-folder {out_folder} \
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  --min_genes 250 \
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  --min_cells 50 \
{gwaslab-3.6.2.dist-info → gwaslab-3.6.3.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: gwaslab
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- Version: 3.6.2
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+ Version: 3.6.3
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  Summary: A collection of handy tools for GWAS SumStats
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  Author-email: Yunye <gwaslab@gmail.com>
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  Project-URL: Homepage, https://cloufield.github.io/gwaslab/
{gwaslab-3.6.2.dist-info → gwaslab-3.6.3.dist-info}/RECORD RENAMED
@@ -6,7 +6,7 @@ gwaslab/bd_get_hapmap3.py,sha256=qWTvIRZsd7F3nT9sN2NSXUsxZJRf5k4HLgJ6kN0qaUc,410
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  gwaslab/cache_manager.py,sha256=HOTnSkCOyGEPLRl90WT8D_6pAdI8d8AzenMIDGuCeWc,28113
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  gwaslab/g_Log.py,sha256=C3Zv-_6c3C9ms8bgQ-ytplz22sjk7euqXYkWr9zNeAs,1573
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  gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- gwaslab/g_Sumstats.py,sha256=SrF5E46wc_CbVz-GgU3VX-vN9EZeJuVRra4kH3NRI8s,43776
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+ gwaslab/g_Sumstats.py,sha256=VowMdFIwYfGABbhrpMRd3OV8HPRwWjYWTU4p6TAn4Q4,43781
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  gwaslab/g_SumstatsMulti.py,sha256=2y8brnKAs5I9tUexQJiFwOsFLC4MyACn7IybvvXsRDU,13828
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  gwaslab/g_SumstatsPair.py,sha256=PmVPGU32degDuU5RDG9igyT1sFAbEDh6alrRulUphyk,13181
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  gwaslab/g_SumstatsSet.py,sha256=AiTISWPfmu8NTGa8j9Yuts8DNw1pEUENYyPoS0HXp5I,29866
@@ -18,13 +18,13 @@ gwaslab/g_meta.py,sha256=pXtSsQfFPv2UJmOxKMmLtcsp_Ku_H73YP7PnlfMd0sg,6472
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  gwaslab/g_meta_update.py,sha256=dWgz4kcq9bvsXycCjfhoYtcJHlEP4HRdYoQ8KFqMyTQ,2490
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  gwaslab/g_vchange_status.py,sha256=w3zsYYOcCaI3PTeboonvkQjudzUAfVIgATzRdiPViZs,1939
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  gwaslab/g_vchange_status_polars.py,sha256=kxyGQCur0ibVFBCyZghA-XNf_kLDXKK-l7VC-Om2IdA,1839
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- gwaslab/g_version.py,sha256=3oGant2IqVAE1geaqXJxCyH2hrdFPJZWH1T5WpDkVdc,1889
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+ gwaslab/g_version.py,sha256=Jop2Odt1nWgJsn3Dghjc76Mmetuwqm1xAqeFva3yVgk,1962
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  gwaslab/hm_casting.py,sha256=xoq1E4Tp5VC4aLWfq9-_AfiQzb1WZAHrnZG33W4sCOE,14178
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  gwaslab/hm_casting_polars.py,sha256=_3ZeMg3mRsa7vHpxObFErOledpaydhC_PxStcwlYO2c,8371
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  gwaslab/hm_harmonize_sumstats.py,sha256=2MeWnWmMHpLWjUMTVqExpg_3mE1VIaBsh6Mz3ffJCMc,84761
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  gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
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- gwaslab/io_load_ld.py,sha256=pJemMmHn5GrEbIloqGPX3tBStjkA6DVrAoerGOUBbqc,21827
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- gwaslab/io_preformat_input.py,sha256=EGSEqoeEtVnUFYV24EeXLkrYjjGZKMxDdpfAmCjp8G8,25661
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+ gwaslab/io_load_ld.py,sha256=P4v-6WO3boamvc3i_iAfwZlo-z4JwBez81S5CkxpoS4,21916
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+ gwaslab/io_preformat_input.py,sha256=3C33kvtPpVfaidWWBDx6Z4Nu60Wj4L80SX80xD_beUY,25713
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  gwaslab/io_preformat_input_polars.py,sha256=HGdi6rXPQnYjTW8fMUds-uF6Lt8uElL3Er_Afv3OjTc,24767
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  gwaslab/io_process_args.py,sha256=TIv0DyaVEcHnLBGdOD52GBZiO6nAQJycAmmVdEYPmRE,1918
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  gwaslab/io_read_ldsc.py,sha256=9tV4AfQZmCAyiNSR9uALmXWOytWhBdT0pfMAY5Mx_QQ,13407
@@ -60,14 +60,14 @@ gwaslab/util_ex_process_h5.py,sha256=ynFvo3zxgvOxWYL565v2IQf8P6iEuq7UlKQ_ULxrd6Y
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  gwaslab/util_ex_process_ref.py,sha256=GQ0ZEWLxGpHLdBs3tqnAqKn3Pqx1A1YvNbYrBLBvXeg,17126
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  gwaslab/util_ex_run_2samplemr.py,sha256=eIw-bHlYpgqgRnAhWIWNTbMplVbH4Dbj9kDyDBtzkT0,10423
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  gwaslab/util_ex_run_ccgwas.py,sha256=8uOAaJ44zAhlxj_A2vth5AzRLk2_BYlYBXEccFbB6T0,5959
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- gwaslab/util_ex_run_clumping.py,sha256=yvUhKi83KhXfE5yPy2i47B58BMACZ_r5gt3-uN8Znbo,7908
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+ gwaslab/util_ex_run_clumping.py,sha256=7JdHP2XmJS1b0yJObxXDKvEXuZ6wezHvvUMFEzVcswY,8081
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  gwaslab/util_ex_run_coloc.py,sha256=evLJ_ct_RV7UKLnYGJ_VfT6MeuGeYDtj8M8xqqk-X-U,6297
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  gwaslab/util_ex_run_hyprcoloc.py,sha256=sElGLXsBKx3PpDTOET7ulvjBShtDOJ3OyDuOp3Yl_y0,4722
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  gwaslab/util_ex_run_magma.py,sha256=40Mr9IIkUXTHa3bBfROORr-5iVre-W8SeoZhHjh7aTo,2436
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  gwaslab/util_ex_run_mesusie.py,sha256=g0x7-zwoN9fbHYJQAue3vAMIeFu3x8H9KjgiYI1u9Mk,5532
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  gwaslab/util_ex_run_mtag.py,sha256=TxfDwjbGy5C1SiTVDMNopcSjl9p5mgCjJVBfeLq__bg,2952
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  gwaslab/util_ex_run_prscs.py,sha256=_BOUqX3fgALdGx-xDyWlREXCafZZddhcK8ufoESUaac,3396
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- gwaslab/util_ex_run_scdrs.py,sha256=_IfWztG8fRYuqClNKiMIGwutDi24d2GtYhjeF6V2jdE,3022
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+ gwaslab/util_ex_run_scdrs.py,sha256=cs1-6QMB2uixa7j97vN7xe3NQ8aQwZ1QAmfj_cc-Kec,3024
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  gwaslab/util_ex_run_susie.py,sha256=YbHishvu7rT83JSHw_Tb_FKzfkZ296YpvNhBesveYR4,6332
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  gwaslab/util_in_calculate_gc.py,sha256=MWOXVzJv7SZx4i2_ncRiqsiEOADc7EfghaUzgGy4jaE,2219
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  gwaslab/util_in_calculate_power.py,sha256=JfHJFg3tNF0f4NHgWlzVW2mSxCiP07mAHIyEfVfxTak,10360
@@ -112,9 +112,9 @@ gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz,sha256=qD9RsC5S2h6l-OdpW
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  gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz,sha256=Y8ZT2FIAhbhlgCJdE9qQVAiwnV_fcsPt72usBa7RSBM,10225828
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  gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz,sha256=R7IkssKu0L4WwkU9SrS84xCMdrkkKL0gnTNO_OKbG0Y,219
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  gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz,sha256=76CIU0pibDJ72Y6UY-TbIKE9gEPwTELAaIbCXyjm80Q,470
115
- gwaslab-3.6.2.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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- gwaslab-3.6.2.dist-info/licenses/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
117
- gwaslab-3.6.2.dist-info/METADATA,sha256=V6dIeyLHIwXppMqbyY8JAZtRK4ra4QGgn2ATIn6AydY,7043
118
- gwaslab-3.6.2.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
119
- gwaslab-3.6.2.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
120
- gwaslab-3.6.2.dist-info/RECORD,,
115
+ gwaslab-3.6.3.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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+ gwaslab-3.6.3.dist-info/licenses/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
117
+ gwaslab-3.6.3.dist-info/METADATA,sha256=tIgPWN8dJTS-x4WFwAhEMN3Ex-XJRqdTZYFd8qM7u3w,7043
118
+ gwaslab-3.6.3.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
119
+ gwaslab-3.6.3.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
120
+ gwaslab-3.6.3.dist-info/RECORD,,
{gwaslab-3.6.2.dist-info → gwaslab-3.6.3.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (80.3.1)
2
+ Generator: setuptools (80.4.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any
5
5