gwaslab 3.4.37__py3-none-any.whl → 3.4.39__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 (57) hide show
  1. gwaslab/bd_common_data.py +6 -3
  2. gwaslab/bd_download.py +9 -9
  3. gwaslab/bd_get_hapmap3.py +43 -9
  4. gwaslab/data/formatbook.json +722 -721
  5. gwaslab/g_Log.py +22 -5
  6. gwaslab/g_Sumstats.py +110 -163
  7. gwaslab/g_SumstatsPair.py +76 -25
  8. gwaslab/g_SumstatsT.py +2 -2
  9. gwaslab/g_Sumstats_summary.py +3 -3
  10. gwaslab/g_version.py +10 -10
  11. gwaslab/hm_casting.py +36 -17
  12. gwaslab/hm_harmonize_sumstats.py +354 -221
  13. gwaslab/hm_rsid_to_chrpos.py +1 -1
  14. gwaslab/io_preformat_input.py +49 -43
  15. gwaslab/io_read_ldsc.py +49 -1
  16. gwaslab/io_to_formats.py +428 -295
  17. gwaslab/ldsc_irwls.py +198 -0
  18. gwaslab/ldsc_jackknife.py +514 -0
  19. gwaslab/ldsc_ldscore.py +417 -0
  20. gwaslab/ldsc_parse.py +294 -0
  21. gwaslab/ldsc_regressions.py +747 -0
  22. gwaslab/ldsc_sumstats.py +629 -0
  23. gwaslab/qc_check_datatype.py +3 -3
  24. gwaslab/qc_fix_sumstats.py +891 -778
  25. gwaslab/util_ex_calculate_ldmatrix.py +31 -13
  26. gwaslab/util_ex_gwascatalog.py +25 -25
  27. gwaslab/util_ex_ldproxyfinder.py +10 -10
  28. gwaslab/util_ex_ldsc.py +189 -0
  29. gwaslab/util_ex_process_ref.py +3 -3
  30. gwaslab/util_ex_run_coloc.py +26 -4
  31. gwaslab/util_in_calculate_gc.py +6 -6
  32. gwaslab/util_in_calculate_power.py +42 -43
  33. gwaslab/util_in_convert_h2.py +8 -8
  34. gwaslab/util_in_fill_data.py +30 -30
  35. gwaslab/util_in_filter_value.py +201 -74
  36. gwaslab/util_in_get_density.py +10 -10
  37. gwaslab/util_in_get_sig.py +445 -71
  38. gwaslab/viz_aux_annotate_plot.py +12 -12
  39. gwaslab/viz_aux_quickfix.py +42 -37
  40. gwaslab/viz_aux_reposition_text.py +10 -7
  41. gwaslab/viz_aux_save_figure.py +18 -8
  42. gwaslab/viz_plot_compare_af.py +32 -33
  43. gwaslab/viz_plot_compare_effect.py +63 -71
  44. gwaslab/viz_plot_miamiplot2.py +34 -26
  45. gwaslab/viz_plot_mqqplot.py +126 -75
  46. gwaslab/viz_plot_qqplot.py +11 -8
  47. gwaslab/viz_plot_regionalplot.py +36 -33
  48. gwaslab/viz_plot_rg_heatmap.py +28 -26
  49. gwaslab/viz_plot_stackedregional.py +40 -21
  50. gwaslab/viz_plot_trumpetplot.py +65 -61
  51. gwaslab-3.4.39.dist-info/LICENSE +674 -0
  52. {gwaslab-3.4.37.dist-info → gwaslab-3.4.39.dist-info}/METADATA +5 -4
  53. gwaslab-3.4.39.dist-info/RECORD +80 -0
  54. gwaslab-3.4.37.dist-info/RECORD +0 -72
  55. /gwaslab-3.4.37.dist-info/LICENSE → /gwaslab-3.4.39.dist-info/LICENSE_before_v3.4.39 +0 -0
  56. {gwaslab-3.4.37.dist-info → gwaslab-3.4.39.dist-info}/WHEEL +0 -0
  57. {gwaslab-3.4.37.dist-info → gwaslab-3.4.39.dist-info}/top_level.txt +0 -0
{gwaslab-3.4.37.dist-info → gwaslab-3.4.39.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: gwaslab
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- Version: 3.4.37
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+ Version: 3.4.39
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  Summary: A collection of handy tools for GWAS SumStats
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  Author-email: Yunye <yunye@gwaslab.com>
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  Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -11,10 +11,11 @@ Classifier: Operating System :: OS Independent
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  Requires-Python: <=3.10,>=3.9
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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+ License-File: LICENSE_before_v3.4.39
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  Requires-Dist: pandas !=1.5,>=1.3
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  Requires-Dist: numpy >=1.21.2
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  Requires-Dist: matplotlib !=3.7.2,>=3.5
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- Requires-Dist: seaborn >=0.11.1
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+ Requires-Dist: seaborn >=0.12
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  Requires-Dist: scipy >=1.12
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  Requires-Dist: pySAM <0.20,>=0.18.1
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  Requires-Dist: Biopython >=1.79
@@ -44,7 +45,7 @@ Note: GWASLab is being updated very frequently for now. I will release the first
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  ## Install
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  ```
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- pip install gwaslab==3.4.35
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+ pip install gwaslab==3.4.39
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  ```
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@@ -138,7 +139,7 @@ mysumstats.plot_mqq()
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  - Sumstats summary: give you a quick overview of the sumstats.
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  - ...
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- ## Requirements
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+ ## Requirements (deprecated)
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  environment.yml
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gwaslab-3.4.39.dist-info/RECORD ADDED
@@ -0,0 +1,80 @@
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+ gwaslab/__init__.py,sha256=dFnrh4L620F5JirsSF98SmkuligA-fybIGdBF6r9Ims,2386
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+ gwaslab/bd_common_data.py,sha256=svW9UxpGyf46YXXAJ1lAZKjF7lnlM9WuRrSCZ3RhLUI,11883
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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=T3P65fIeNwhdlpdlMaggasFPJGTYMxVcip-IFl_yziE,3606
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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=AB_Gd1Cqd0fKXflQSu03gE-jUN-QBt05rZ6DycnKAbo,32554
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+ gwaslab/g_SumstatsPair.py,sha256=MjuTVrluTWjUDFg4WitnzNzxNr9_HhffYBNHOrzpcJM,8803
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+ gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
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+ gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
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+ gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
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+ gwaslab/g_vchange_status.py,sha256=eX0jdIb6Spa07ZdpWNqUWqdVBWS0fuH2yrt4PDi3Res,1746
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+ gwaslab/g_version.py,sha256=iA4PPyz59J_e3sihzN1Pawx07gM9nwHDrCw9s7UdC6I,1820
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+ gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
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+ gwaslab/hm_harmonize_sumstats.py,sha256=PjSUQchp7416joy4P65Jxcr75RFhSBXVLMRwvAMpEsg,47576
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+ gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
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+ gwaslab/io_preformat_input.py,sha256=w62JLAr16Ru0EgUtBCEV2eXRO89OqhidQxwf2IPAM38,20014
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+ gwaslab/io_read_ldsc.py,sha256=ypApII8IW0UWkYpR_O__HScPytmD7wEf4GH5os_QCX4,10352
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+ gwaslab/io_read_tabular.py,sha256=_gI0EA4CDecTPHTDp6hW2PesagYHHbBQvI_tW8U3Tc8,2366
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+ gwaslab/io_to_formats.py,sha256=cvnRoZd1o1__FTx5b8tVmZOf1BV1vhO_k09Jkm8yhRA,26221
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+ gwaslab/io_to_pickle.py,sha256=XmxhV5-38ED8aEyPYzsskv7HrxCyge9tHJ2F21QA8Ms,1824
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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=UF4F5ZNC6TbGUWA0bk3tDnBWlCRHklvUXYhhNR8rWaY,14573
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+ gwaslab/ldsc_parse.py,sha256=E_5PhKQfKpOhuuMT9ZL-ciLfeNJReMG_WulAKu8FoeI,10511
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+ gwaslab/ldsc_regressions.py,sha256=yzbGjgNV7u-SWXNPsh9S8y9mK97Bim_Nmad9G9V18ZU,30078
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+ gwaslab/ldsc_sumstats.py,sha256=9X86tFPgz2JZmsFkxM5yyfTjC6_PYUVre8RlXygozbE,26074
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+ gwaslab/qc_check_datatype.py,sha256=kW68uk4dTLOU2b1dHoVat6n0loundDysAjIqxsXW28Q,3379
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+ gwaslab/qc_fix_sumstats.py,sha256=E4xsKOaUvFN2m25I9A-qhfbHSrCISYql4-pf3LjfNmI,87202
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+ gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ gwaslab/util_ex_calculate_ldmatrix.py,sha256=B5VRaV9vpcFY_yKciuwzC8MYSpKhVb2JXzDHFkBOtiQ,13054
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+ gwaslab/util_ex_calculate_prs.py,sha256=uOcMRWujEYMYGuO-qGe3okQJYizXGvqDcomXlzLvln8,9049
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+ gwaslab/util_ex_gwascatalog.py,sha256=--Gde9HrsikfYTeFqSaYz0gUODr9wmv_gV6GZGNlElg,7688
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+ gwaslab/util_ex_ldproxyfinder.py,sha256=o1QTq-Sp_wO04GEOIPi3Ymp0V-_RJujHzVeiO9bZe5w,9432
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+ gwaslab/util_ex_ldsc.py,sha256=7RaEfYREcMUcOB5gCddDXxBqYjRxYL11fCso_2UjLeQ,7251
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+ gwaslab/util_ex_plink_filter.py,sha256=Ak09-tEIS_uq1OtiCmcDCXcEjzQHCEfp44AKkhgoOzY,1669
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+ gwaslab/util_ex_process_h5.py,sha256=1QzcQurnwedYFiF4ZaEOv0Wl41rBEUjS7yVcMWNIslE,2741
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+ gwaslab/util_ex_process_ref.py,sha256=Y_nyWzhW1mOGSWvaTuNA3dJ8_QTbu0ETGnH73NOHI5g,16464
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+ gwaslab/util_ex_run_2samplemr.py,sha256=AvhpR_ihR052LBabR1wfEaBqfwCs88VW8Q2ijdKMfUs,9040
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+ gwaslab/util_ex_run_clumping.py,sha256=fE-PHeYjl8I08ycwCbJrQjF3wixMDYKNe4EASupEMpo,6816
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+ gwaslab/util_ex_run_coloc.py,sha256=TXk0zZz4KmVV_nm5RDnXycUBu0TA3xfmTRdwJb7g_ic,6198
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+ gwaslab/util_ex_run_susie.py,sha256=fxs5eCxA48j62dZlgTAPk8FMEIH7NK9cQxoy_s8RbdY,4252
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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=o7CjUwLp4B_60yrntV76ESNaoPcl-HPOzSw9cYWzpW4,2050
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+ gwaslab/util_in_fill_data.py,sha256=gdTwYA6FvBMnrtxAeL0lEj_Z0aGIoRNPScWDlJvZWeQ,14021
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+ gwaslab/util_in_filter_value.py,sha256=VObRMOEJsylSoLPzyKoi54nxlgcCtuHu-f28pBuouS4,20044
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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=yZwLhbp_owAX3dvkKsPg4fmkr_c3vk_hMgZzmfuTQw8,37178
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+ gwaslab/viz_aux_annotate_plot.py,sha256=R-1GT89E4NEBAMNTYzNawdi9rjQV5LCnODgnYOOKsys,32184
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+ gwaslab/viz_aux_quickfix.py,sha256=Z6ZNEAUFuWVDTzH-qGreNGxPxJLCmqhXtBrvDOgo4g8,18308
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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=nL-aoE8Kg06h7FgleGRBIZjhI-6w5gpn3E1HWMwBig8,2664
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+ gwaslab/viz_plot_compare_af.py,sha256=qtXW45-Sq_ugK8ZfqBYMpmf58SKi3lB3YyHnzn_akcE,5344
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+ gwaslab/viz_plot_compare_effect.py,sha256=8om3y6YQfnOk4FfkKSpKr2KqJcsMeCwQ6FRRKbDrm3U,49366
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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_miamiplot2.py,sha256=SWv82D8UBbREKsk8EoKth-2w68l6FbXyVLsb_E1hh8o,15882
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+ gwaslab/viz_plot_mqqplot.py,sha256=xIx-m8IP0GAAKuIoiAbzxl3fkUDEEunczo6dVEZ3KRY,61671
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+ gwaslab/viz_plot_qqplot.py,sha256=psQgVpP29686CEZkzQz0iRbApzqy7aE3GGiBcazVvNw,7247
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+ gwaslab/viz_plot_regionalplot.py,sha256=Lt5mfPfQQnlN7JEMY-Yqyqits-KaAF3cz_MMFPOAD2o,37625
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+ gwaslab/viz_plot_rg_heatmap.py,sha256=PidUsgOiEVt6MfBPCF3_yDhOEytZ-I1q-ZD6_0pFrV4,13713
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+ gwaslab/viz_plot_stackedregional.py,sha256=EAHz5SZGengZ_pxcOg62ZRimGRz6_goQlp9MLCwmeZc,11890
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+ gwaslab/viz_plot_trumpetplot.py,sha256=36XKPBrS0lOTFs15oEJPgeNCUE17JNLhlT14SuwbTVw,37472
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+ gwaslab/data/formatbook.json,sha256=N2nJs80HH98Rsu9FxaSvIQO9J5yIV97WEtAKjRqYwiY,38207
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+ gwaslab/data/reference.json,sha256=k8AvvgDsuLxzv-NCJHWvTUZ5q_DLAFxs1Th3jtL313k,11441
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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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+ gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz,sha256=qD9RsC5S2h6l-OdpW09DWXHIi2kcPebctMnhxt8mzfU,10282886
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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
75
+ gwaslab-3.4.39.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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+ gwaslab-3.4.39.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
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+ gwaslab-3.4.39.dist-info/METADATA,sha256=fQjJUc2oVJsKEWrGkAPu6dfahnBDa3SXR1nPvX9Xj5g,6854
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+ gwaslab-3.4.39.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
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+ gwaslab-3.4.39.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
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+ gwaslab-3.4.39.dist-info/RECORD,,
gwaslab-3.4.37.dist-info/RECORD DELETED
@@ -1,72 +0,0 @@
1
- gwaslab/__init__.py,sha256=dFnrh4L620F5JirsSF98SmkuligA-fybIGdBF6r9Ims,2386
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- gwaslab/bd_common_data.py,sha256=-YlytsRU3YnwI23EV0U_pFWZ0_0yL23_RwTfBajEuPw,11844
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- gwaslab/bd_config.py,sha256=TP-r-DPhJD3XnRYZbw9bQHXaDIkiRgK8bG9HCt-UaLc,580
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- gwaslab/bd_download.py,sha256=Nh09FP_d5kLsAyEF-WOYd7tty-ypvJv0PSTEO4JB2cc,15636
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- gwaslab/bd_get_hapmap3.py,sha256=poqV3Ko56xhRFKdSK0ROwDQ71b27-9bMOQ0XO36To5c,2034
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- gwaslab/g_Log.py,sha256=ICCzc2iP-toIRhXSnRufMqJrB6MtstJXk5qmC2yK6pY,821
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- gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- gwaslab/g_Sumstats.py,sha256=9Qu5RFKgeZIkhHp-YwYZcECQOLV8dOGHvx2y9YVO3LA,33210
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- gwaslab/g_SumstatsPair.py,sha256=eFFcL0foi7KJ2t7yf98WIyUMv-Kl6IrvSdv3FtqZmXs,5971
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- gwaslab/g_SumstatsT.py,sha256=r3fAN-LsUIJhi7mhLH_4NBwHCOawVkbWULKY1vbmdZY,2113
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- gwaslab/g_Sumstats_summary.py,sha256=Q69702tABxTVk6QIbqQ4k6eSujhXr_MVVQ5saOdEhlk,6367
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- gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
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- gwaslab/g_vchange_status.py,sha256=eX0jdIb6Spa07ZdpWNqUWqdVBWS0fuH2yrt4PDi3Res,1746
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- gwaslab/g_version.py,sha256=nM7GpPDOdGl2i6-JJyZDrSlJfCCWoq9dFIfHrTcQTQg,1688
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- gwaslab/hm_casting.py,sha256=w8Qz0IlFwmn4_uUc7aOccWZCfY_e19ZZr-iYgCu-SnQ,10350
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- gwaslab/hm_harmonize_sumstats.py,sha256=l8kHWVJkveRfzeKjvh6Mx5Z_QLy52GSL_9euYnFtH-U,41692
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- gwaslab/hm_rsid_to_chrpos.py,sha256=-pKhY654zS4uULW7FP4yGHNy3e9Wc2ujc1VLBaoUO5A,6564
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- gwaslab/io_preformat_input.py,sha256=vusQAi9vR1Bn8K4Zf9KmDwuwqrhSaAZNZ4zHp6yfjxY,19625
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- gwaslab/io_read_ldsc.py,sha256=mro3Vc3dQs6dQ2zsUaUYHOqJGIhJaNzxPeE3zsfO7dA,8659
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- gwaslab/io_read_tabular.py,sha256=_gI0EA4CDecTPHTDp6hW2PesagYHHbBQvI_tW8U3Tc8,2366
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- gwaslab/io_to_formats.py,sha256=tayh5qoxe9tn_g3mHTbfT3Jkz7kTo8BOPjpMtoMlfAY,21111
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- gwaslab/io_to_pickle.py,sha256=XmxhV5-38ED8aEyPYzsskv7HrxCyge9tHJ2F21QA8Ms,1824
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