gwaslab 3.4.42__tar.gz → 3.4.43__tar.gz

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.

Potentially problematic release.

This version of gwaslab might be problematic. Click here for more details.

Files changed (86) hide show
  1. {gwaslab-3.4.42/src/gwaslab.egg-info → gwaslab-3.4.43}/PKG-INFO +3 -1
  2. {gwaslab-3.4.42 → gwaslab-3.4.43}/README.md +1 -0
  3. {gwaslab-3.4.42 → gwaslab-3.4.43}/pyproject.toml +3 -2
  4. gwaslab-3.4.43/src/gwaslab/cache_manager.py +687 -0
  5. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/g_version.py +2 -2
  6. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/hm_harmonize_sumstats.py +193 -20
  7. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/qc_fix_sumstats.py +2 -9
  8. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_mqqplot.py +12 -11
  9. {gwaslab-3.4.42 → gwaslab-3.4.43/src/gwaslab.egg-info}/PKG-INFO +3 -1
  10. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab.egg-info/SOURCES.txt +1 -0
  11. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab.egg-info/requires.txt +1 -0
  12. {gwaslab-3.4.42 → gwaslab-3.4.43}/LICENSE +0 -0
  13. {gwaslab-3.4.42 → gwaslab-3.4.43}/LICENSE_before_v3.4.39 +0 -0
  14. {gwaslab-3.4.42 → gwaslab-3.4.43}/setup.cfg +0 -0
  15. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/__init__.py +0 -0
  16. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/bd_common_data.py +0 -0
  17. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/bd_config.py +0 -0
  18. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/bd_download.py +0 -0
  19. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/bd_get_hapmap3.py +0 -0
  20. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/data/chrx_par/chrx_par_hg19.bed.gz +0 -0
  21. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/data/chrx_par/chrx_par_hg38.bed.gz +0 -0
  22. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/data/formatbook.json +0 -0
  23. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz +0 -0
  24. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz +0 -0
  25. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz +0 -0
  26. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz +0 -0
  27. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/data/reference.json +0 -0
  28. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/g_Log.py +0 -0
  29. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/g_Phenotypes.py +0 -0
  30. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/g_Sumstats.py +0 -0
  31. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/g_SumstatsPair.py +0 -0
  32. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/g_SumstatsT.py +0 -0
  33. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/g_Sumstats_summary.py +0 -0
  34. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/g_meta.py +0 -0
  35. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/g_vchange_status.py +0 -0
  36. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/hm_casting.py +0 -0
  37. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/hm_rsid_to_chrpos.py +0 -0
  38. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/io_preformat_input.py +0 -0
  39. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/io_read_ldsc.py +0 -0
  40. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/io_read_tabular.py +0 -0
  41. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/io_to_formats.py +0 -0
  42. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/io_to_pickle.py +0 -0
  43. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/ldsc_irwls.py +0 -0
  44. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/ldsc_jackknife.py +0 -0
  45. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/ldsc_ldscore.py +0 -0
  46. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/ldsc_parse.py +0 -0
  47. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/ldsc_regressions.py +0 -0
  48. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/ldsc_sumstats.py +0 -0
  49. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/qc_check_datatype.py +0 -0
  50. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/run_script.py +0 -0
  51. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_calculate_ldmatrix.py +0 -0
  52. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_calculate_prs.py +0 -0
  53. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_gwascatalog.py +0 -0
  54. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_ldproxyfinder.py +0 -0
  55. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_ldsc.py +0 -0
  56. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_plink_filter.py +0 -0
  57. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_process_h5.py +0 -0
  58. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_process_ref.py +0 -0
  59. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_run_2samplemr.py +0 -0
  60. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_run_clumping.py +0 -0
  61. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_run_coloc.py +0 -0
  62. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_ex_run_susie.py +0 -0
  63. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_in_calculate_gc.py +0 -0
  64. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_in_calculate_power.py +0 -0
  65. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_in_convert_h2.py +0 -0
  66. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_in_correct_winnerscurse.py +0 -0
  67. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_in_fill_data.py +0 -0
  68. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_in_filter_value.py +0 -0
  69. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_in_get_density.py +0 -0
  70. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/util_in_get_sig.py +0 -0
  71. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_aux_annotate_plot.py +0 -0
  72. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_aux_quickfix.py +0 -0
  73. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_aux_reposition_text.py +0 -0
  74. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_aux_save_figure.py +0 -0
  75. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_compare_af.py +0 -0
  76. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_compare_effect.py +0 -0
  77. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_forestplot.py +0 -0
  78. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_miamiplot.py +0 -0
  79. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_miamiplot2.py +0 -0
  80. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_qqplot.py +0 -0
  81. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_regionalplot.py +0 -0
  82. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_rg_heatmap.py +0 -0
  83. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_stackedregional.py +0 -0
  84. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab/viz_plot_trumpetplot.py +0 -0
  85. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab.egg-info/dependency_links.txt +0 -0
  86. {gwaslab-3.4.42 → gwaslab-3.4.43}/src/gwaslab.egg-info/top_level.txt +0 -0
{gwaslab-3.4.42/src/gwaslab.egg-info → gwaslab-3.4.43}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: gwaslab
3
- Version: 3.4.42
3
+ Version: 3.4.43
4
4
  Summary: A collection of handy tools for GWAS SumStats
5
5
  Author-email: Yunye <yunye@gwaslab.com>
6
6
  Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -24,6 +24,7 @@ Requires-Dist: liftover>=1.1.13
24
24
  Requires-Dist: scikit-allel>=1.3.5
25
25
  Requires-Dist: pyensembl==2.2.3
26
26
  Requires-Dist: gtfparse==1.3.0
27
+ Requires-Dist: h5py>=3.10.0
27
28
 
28
29
  # GWASLab
29
30
 
@@ -193,6 +194,7 @@ dependencies:
193
194
  - adjustText==0.8
194
195
  - pysam==0.19
195
196
  - pyensembl==2.2.3
197
+ - h5py==3.10.0
196
198
  ```
197
199
 
198
200
  ## How to cite
{gwaslab-3.4.42 → gwaslab-3.4.43}/README.md RENAMED
@@ -166,6 +166,7 @@ dependencies:
166
166
  - adjustText==0.8
167
167
  - pysam==0.19
168
168
  - pyensembl==2.2.3
169
+ - h5py==3.10.0
169
170
  ```
170
171
 
171
172
  ## How to cite
{gwaslab-3.4.42 → gwaslab-3.4.43}/pyproject.toml RENAMED
@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
7
7
 
8
8
  [project]
9
9
  name = "gwaslab"
10
- version = "3.4.42"
10
+ version = "3.4.43"
11
11
  authors = [
12
12
  { name="Yunye", email="yunye@gwaslab.com" },
13
13
  ]
@@ -27,7 +27,8 @@ dependencies = [
27
27
  "liftover>=1.1.13",
28
28
  "scikit-allel>=1.3.5",
29
29
  "pyensembl==2.2.3",
30
- "gtfparse==1.3.0"
30
+ "gtfparse==1.3.0",
31
+ "h5py>=3.10.0"
31
32
  ]
32
33
 
33
34
  requires-python = ">=3.9,<=3.10"