gwaslab 3.5.7__py3-none-any.whl → 3.6.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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Files changed (67) hide show
  1. gwaslab/__init__.py +2 -0
  2. gwaslab/bd_common_data.py +1 -0
  3. gwaslab/bd_get_hapmap3.py +0 -1
  4. gwaslab/data/formatbook.json +78 -0
  5. gwaslab/data/reference.json +3 -1
  6. gwaslab/g_Sumstats.py +110 -25
  7. gwaslab/g_SumstatsMulti.py +287 -0
  8. gwaslab/g_SumstatsPair.py +101 -16
  9. gwaslab/g_Sumstats_polars.py +245 -0
  10. gwaslab/g_headers.py +12 -3
  11. gwaslab/g_meta.py +124 -47
  12. gwaslab/g_meta_update.py +48 -0
  13. gwaslab/g_vchange_status_polars.py +44 -0
  14. gwaslab/g_version.py +2 -2
  15. gwaslab/hm_casting.py +169 -110
  16. gwaslab/hm_casting_polars.py +202 -0
  17. gwaslab/hm_harmonize_sumstats.py +19 -8
  18. gwaslab/io_load_ld.py +529 -0
  19. gwaslab/io_preformat_input.py +11 -0
  20. gwaslab/io_preformat_input_polars.py +632 -0
  21. gwaslab/io_process_args.py +25 -1
  22. gwaslab/io_read_ldsc.py +34 -3
  23. gwaslab/io_read_pipcs.py +62 -6
  24. gwaslab/prscs_gigrnd.py +122 -0
  25. gwaslab/prscs_mcmc_gtb.py +136 -0
  26. gwaslab/prscs_parse_genet.py +98 -0
  27. gwaslab/qc_build.py +53 -0
  28. gwaslab/qc_check_datatype.py +10 -8
  29. gwaslab/qc_check_datatype_polars.py +128 -0
  30. gwaslab/qc_fix_sumstats.py +25 -23
  31. gwaslab/qc_fix_sumstats_polars.py +193 -0
  32. gwaslab/util_ex_calculate_ldmatrix.py +49 -19
  33. gwaslab/util_ex_gwascatalog.py +71 -28
  34. gwaslab/util_ex_infer_ancestry.py +65 -0
  35. gwaslab/util_ex_ldsc.py +67 -21
  36. gwaslab/util_ex_match_ldmatrix.py +396 -0
  37. gwaslab/util_ex_run_2samplemr.py +0 -2
  38. gwaslab/util_ex_run_ccgwas.py +155 -0
  39. gwaslab/util_ex_run_coloc.py +1 -1
  40. gwaslab/util_ex_run_hyprcoloc.py +117 -0
  41. gwaslab/util_ex_run_magma.py +74 -0
  42. gwaslab/util_ex_run_mesusie.py +155 -0
  43. gwaslab/util_ex_run_mtag.py +92 -0
  44. gwaslab/util_ex_run_prscs.py +85 -0
  45. gwaslab/util_ex_run_susie.py +40 -9
  46. gwaslab/util_in_estimate_ess.py +18 -0
  47. gwaslab/util_in_fill_data.py +20 -1
  48. gwaslab/util_in_filter_value.py +10 -5
  49. gwaslab/util_in_get_sig.py +71 -13
  50. gwaslab/util_in_meta.py +168 -4
  51. gwaslab/util_in_meta_polars.py +174 -0
  52. gwaslab/viz_aux_annotate_plot.py +13 -2
  53. gwaslab/viz_plot_compare_effect.py +87 -23
  54. gwaslab/viz_plot_credible_sets.py +55 -11
  55. gwaslab/viz_plot_effect.py +22 -12
  56. gwaslab/viz_plot_miamiplot2.py +3 -2
  57. gwaslab/viz_plot_mqqplot.py +94 -84
  58. gwaslab/viz_plot_qqplot.py +9 -7
  59. gwaslab/viz_plot_regional2.py +2 -1
  60. gwaslab/viz_plot_stackedregional.py +4 -1
  61. {gwaslab-3.5.7.dist-info → gwaslab-3.6.0.dist-info}/METADATA +46 -68
  62. gwaslab-3.6.0.dist-info/RECORD +119 -0
  63. {gwaslab-3.5.7.dist-info → gwaslab-3.6.0.dist-info}/WHEEL +1 -1
  64. gwaslab-3.5.7.dist-info/RECORD +0 -96
  65. {gwaslab-3.5.7.dist-info → gwaslab-3.6.0.dist-info/licenses}/LICENSE +0 -0
  66. {gwaslab-3.5.7.dist-info → gwaslab-3.6.0.dist-info/licenses}/LICENSE_before_v3.4.39 +0 -0
  67. {gwaslab-3.5.7.dist-info → gwaslab-3.6.0.dist-info}/top_level.txt +0 -0
@@ -0,0 +1,119 @@
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+ gwaslab/__init__.py,sha256=Lpa15i924wRu1jZ9_B2Tz5724FQkdb9O5Wg3tQPWR68,2683
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+ gwaslab/bd_common_data.py,sha256=jqkdKib-tc8RKyYMPy8z2KF3YwCWIr-6STMCi4xR7KY,13899
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+ gwaslab/bd_config.py,sha256=TP-r-DPhJD3XnRYZbw9bQHXaDIkiRgK8bG9HCt-UaLc,580
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+ gwaslab/bd_download.py,sha256=cDDk2C5IvjeAzvPvVYGTkI4Ss33DUtEDjGo8eAbQRvY,15663
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+ gwaslab/bd_get_hapmap3.py,sha256=qWTvIRZsd7F3nT9sN2NSXUsxZJRf5k4HLgJ6kN0qaUc,4107
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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=l1zmEOifAZvnv7BoLzyLcTV6Yp1KX5n5HH930GQ9xlE,43502
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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
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+ gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
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+ gwaslab/g_Sumstats_polars.py,sha256=F9d8y-6SJLRibrZrvWtwE2XpxZdG3A9DqqTT8TW4sS0,8528
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+ gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
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+ gwaslab/g_headers.py,sha256=B0bTVqzf2pdUwAX1U8MoYDO7nQEKAtgVnn-9bVXsJGE,6766
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+ 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=o8J0x9TeG_k6wUFeFHrx1HQA4JK3mxYQakjlpBACIX8,1889
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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_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
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+ gwaslab/io_read_pipcs.py,sha256=MPkdVDff_JTmoBCDswg_GO0UQ1tFas2rI0jLuMRqRjY,2891
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+ gwaslab/io_read_tabular.py,sha256=EG-C6KhCutt4J4LlOMgXnqzJvU-EZXzVhMvaDFnHrMM,2380
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+ gwaslab/io_to_formats.py,sha256=uAmZ4xzVoJqXGXxwTZlbppli4fPc2EshnuTJm2DC4v8,32799
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+ gwaslab/io_to_pickle.py,sha256=HhePU0VcaGni0HTNU0BqoRaOnrr0NOxotgY6ISdx3Ck,1833
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+ gwaslab/ldsc_irwls.py,sha256=83JbAMAhD0KOfpv4IJa6LgUDfQjp4XSJveTjnhCBJYQ,6142
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+ gwaslab/ldsc_jackknife.py,sha256=XrWHoKS_Xn9StG1I83S2vUMTertsb-GH-_gOFYUhLeU,17715
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+ gwaslab/ldsc_ldscore.py,sha256=ZOxMvV3PhZzLsTmkKQqjabk_9PdrCTtPhbrdrpGmRAk,14580
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+ gwaslab/ldsc_parse.py,sha256=MBnfgcWlV4oHp9MoDRh1mpilaHhAR15Af77hMFn4-5k,10564
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+ gwaslab/ldsc_regressions.py,sha256=yzbGjgNV7u-SWXNPsh9S8y9mK97Bim_Nmad9G9V18ZU,30078
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+ gwaslab/ldsc_sumstats.py,sha256=O0olsDxKlh1MJ1gAuEN1t40rxhajOEwOQ20ak7xoDrI,26245
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+ gwaslab/prscs_gigrnd.py,sha256=oKv3lN0AJjg-Vm39_qMzVZ-iux5rVWBUU1meJv4iEs8,2872
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+ gwaslab/prscs_mcmc_gtb.py,sha256=QdwUY0V4D1eEfgZVO_XRrnXcShkbBZcCAZgLdeXPJVI,4607
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+ gwaslab/prscs_parse_genet.py,sha256=N7UmyvdO--yTKvbjMNQCVucRIs4PbRGf93maGkh8PP4,3137
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+ gwaslab/qc_build.py,sha256=oeJqV-zbn-9FZ7SsmT4DPuYTt_IIeXw0XtmEkSzN5qA,2145
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+ gwaslab/qc_check_datatype.py,sha256=XuL4sg-OkdIiGaHg98JHZems0Uo-OyF5DlUTyE9gUd4,4580
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+ gwaslab/qc_check_datatype_polars.py,sha256=rJ1dIruxclHi37zd5xpS1ml30-200NI-FoEAVTe9_Eo,4218
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+ gwaslab/qc_fix_sumstats.py,sha256=7l4kjmllaX7Wfq81F2tnF4klijW42j0KaaJeNPJhTYs,98369
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+ gwaslab/qc_fix_sumstats_polars.py,sha256=5DY2PkWiZdfY-k8jXW69YnYPUmJiAw8uaolG8Oztr5g,9600
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+ gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ gwaslab/util_abf_finemapping.py,sha256=LRcopjtkT-iXtKPAJIzR4qjPdhD7nrS_BGit4EW89FM,3054
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+ gwaslab/util_ex_calculate_ldmatrix.py,sha256=TeXazNXInGYrBR58Q3-f51yrHz5-_A3tXNieYJA2-i8,16924
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+ gwaslab/util_ex_calculate_prs.py,sha256=9uJ588Sdj4V0vw3OZ9NeLECwOvW67f0IdLandVPS5RY,9442
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+ gwaslab/util_ex_gwascatalog.py,sha256=RZ_qIsfjONUbF3AGMp-0feTBubOEEZUufYGdvv0Sk7g,9211
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+ gwaslab/util_ex_infer_ancestry.py,sha256=AXLEhuJUBT6XIYjADB-envFRGIZ-misnegGdtK8SsFc,2192
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+ gwaslab/util_ex_ldproxyfinder.py,sha256=HadmnjEv5EvZCHR5SFSAbqxZWJryEErJftCS0WhZUbs,16898
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+ gwaslab/util_ex_ldsc.py,sha256=uEVrsGrT5A-ni7Vw7esvqQ7NwiR1P10Q_N1_uZNRzRY,21600
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+ gwaslab/util_ex_match_ldmatrix.py,sha256=8nFziC8LiUy83bG9vW_u_CzbZek-9R9eVIfFdRBDkrA,17495
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+ gwaslab/util_ex_plink_filter.py,sha256=pK1Yxtv9-J4rMOdVAG7VU9PktvI6-y4FxBiVEH0QuRs,1673
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+ gwaslab/util_ex_process_h5.py,sha256=ynFvo3zxgvOxWYL565v2IQf8P6iEuq7UlKQ_ULxrd6Y,2831
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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_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=0vUac7iVySnRx8QoYBncSfIEke5MwTfmYzDLcSmw1Us,2439
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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_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
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+ gwaslab/util_in_convert_h2.py,sha256=a8Cbudt3xn9WP2bPc-7ysuowB-LYub8j8GeDXl7Lk7Q,6483
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+ gwaslab/util_in_correct_winnerscurse.py,sha256=Gp--yAQ8MMzdkWIvXP9C1BHVjZc-YzqHfYWhAj19w9w,2110
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+ gwaslab/util_in_estimate_ess.py,sha256=QDOQ5vXfHtVkUEqX-TscsC831-FMTtGXXiHo1YxSFzU,1009
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+ gwaslab/util_in_fill_data.py,sha256=hhH1teiQEOAZMOCtAe_de9NREUMnP5l2VrXK8_QR564,16595
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+ gwaslab/util_in_filter_value.py,sha256=dr1ZiTsMoYZKznQtucHBFW2mVYOv9OTESb24vXNcS0U,26648
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+ gwaslab/util_in_get_density.py,sha256=kpKXH69acMkeYVG5vs-VbJC3COhmuLBfYco-wuOxgjc,3934
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+ gwaslab/util_in_get_sig.py,sha256=jOMdDu1iWq5-qs8crHLNvn4t12VHSGQp0kG-ce2l3pQ,42441
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+ gwaslab/util_in_merge.py,sha256=KB5VKRTUUZ1XGYUxgCP_l3cWYanjthMdwiZ_DincCZQ,2020
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+ gwaslab/util_in_meta.py,sha256=3OxpnigfaShV7995-1HCbGCwdIjSbsDhC2X7hnT28jo,18712
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+ gwaslab/util_in_meta_polars.py,sha256=i_2DGSDX8KlR3gtuDPXw88a_rbGYWIb58J1MGDMbJx8,8426
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+ gwaslab/util_in_snphwe.py,sha256=-KpIDx6vn_nah6H55IkV2OyjXQVXV13XyBL069WE1wM,1751
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+ gwaslab/viz_aux_annotate_plot.py,sha256=IyGhqFQofrVW9A8UxJ5oNVH96czQ-2_i4s1lVvf2hww,25696
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+ gwaslab/viz_aux_chromatin.py,sha256=aWZaXOSvGyZY7wQcoFDaqHRYCSHZbi_K4Q70HruN9ts,4125
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+ gwaslab/viz_aux_property.py,sha256=UIaivghnLXYpTwkKnXRK0F28Jbn9L6OaICk3K73WZaU,33
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+ gwaslab/viz_aux_quickfix.py,sha256=cGX5i3WBmvKIiqck8V00caDg-pvKOO709Ux3DBXsUrM,18693
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+ gwaslab/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1eHk04M,4304
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+ gwaslab/viz_aux_save_figure.py,sha256=HwIRDMYpeXfkBgb7mqzLN7OVPMz163U-ZVOlQJABzeg,2811
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+ gwaslab/viz_plot_compare_af.py,sha256=qtXW45-Sq_ugK8ZfqBYMpmf58SKi3lB3YyHnzn_akcE,5344
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+ gwaslab/viz_plot_credible_sets.py,sha256=RC5ZsuW8-0w0S1h4c--PZrYwfHfgZ3clM-9JcoMLJWk,5841
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+ gwaslab/viz_plot_effect.py,sha256=qbM6c1IB2HlUlMNgFZlJ5G8ODQJ8-oSWD8t0Q8DDuz8,10653
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+ gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
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+ gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
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+ gwaslab/viz_plot_mqqplot.py,sha256=mlcsA_wEnv7N9mP6CVL15WXWHJ0-8TwqHuznJXgPwCE,71103
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+ gwaslab/viz_plot_phe_heatmap.py,sha256=qoXVeFTIm-n8IinNbDdPFVBSz2yGCGK6QzTstXv6aj4,9532
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+ gwaslab/viz_plot_qqplot.py,sha256=cB4vRlFv69zWY9NMLfSkfAbirYp3_EEW2kQiBTEMDoc,7483
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+ gwaslab/viz_plot_regional2.py,sha256=BoL1V56ww9B2_vFkABgln_f6OrzobiFjUISI5X6XXMM,43146
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+ gwaslab/viz_plot_regionalplot.py,sha256=8u-5-yfy-UaXhaxVVz3Y5k2kBAoqzczUw1hyyD450iI,37983
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+ gwaslab/viz_plot_rg_heatmap.py,sha256=z-G4gxK5-H_e13jV8RQnNzXPrKSQ0c7q41-KpMrA-cs,13861
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+ gwaslab/viz_plot_scatter_with_reg.py,sha256=PmUZDQl2q4Dme3HLPXEwf_TrMjwJADA-uFXNDBWUEa4,8333
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+ gwaslab/viz_plot_stackedregional.py,sha256=Jzu5NvX45L4iTLfzXjNkxeaA9SGggtGGxEJdGUzSsuU,19163
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+ gwaslab/viz_plot_trumpetplot.py,sha256=y4sAFjzMaSLuWrdr9_ao-wPYCK5DlP2ykiqulWsoN_k,42680
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+ gwaslab/data/formatbook.json,sha256=j6XRTlJvqex4HLBtGLhiaU8JV4_cD1LWl9uqB3Oou4s,40718
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+ gwaslab/data/reference.json,sha256=oaE_HLFeYuEpcZ_rCGY3GwiAJWsDxRtjJOAc188WG28,12620
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+ gwaslab/data/chrx_par/chrx_par_hg19.bed.gz,sha256=LocZg_ozhZjQiIpgWCO4EYCW9xgkEKpRy1m-YdIpzQs,83
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+ gwaslab/data/chrx_par/chrx_par_hg38.bed.gz,sha256=VFW11MnQVC-Iu-ZGvUDcEhVpb-HVRsVTg-W-GNJyxP4,82
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