gwaslab 3.4.42__py3-none-any.whl → 3.4.44__py3-none-any.whl

gwaslab/viz_plot_mqqplot.py

@@ -1031,17 +1031,18 @@ def mqqplot(insumstats,
 
 def _add_pad_to_x_axis(ax1, xpad, xpadl, xpadr, sumstats):
     
-    xmin, xmax = ax1.get_xlim() 
-    
-    if xpad is not None:
-        pad = xpad* sumstats["i"].max()
-        ax1.set_xlim([xmin - pad, xmin + pad])
-    if xpadl is not None:
-        pad = xpadl* sumstats["i"].max()
-        ax1.set_xlim([xmin - pad,xmax])
-    if xpadr is not None:
-        pad = xpadr* sumstats["i"].max()
-        ax1.set_xlim([xmin, xmax + pad])
+    if ax1 is not None:
+        xmin, xmax = ax1.get_xlim() 
+        
+        if xpad is not None:
+            pad = xpad* sumstats["i"].max()
+            ax1.set_xlim([xmin - pad, xmin + pad])
+        if xpadl is not None:
+            pad = xpadl* sumstats["i"].max()
+            ax1.set_xlim([xmin - pad,xmax])
+        if xpadr is not None:
+            pad = xpadr* sumstats["i"].max()
+            ax1.set_xlim([xmin, xmax + pad])
 
     return ax1
 

{gwaslab-3.4.42.dist-info → gwaslab-3.4.44.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.42
+Version: 3.4.44
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -24,6 +24,7 @@ Requires-Dist: liftover >=1.1.13
 Requires-Dist: scikit-allel >=1.3.5
 Requires-Dist: pyensembl ==2.2.3
 Requires-Dist: gtfparse ==1.3.0
+Requires-Dist: h5py >=3.10.0
 
 # GWASLab
 
@@ -50,7 +51,7 @@ Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/
 ### install via pip
 
 ```
-pip install gwaslab==3.4.41
+pip install gwaslab==3.4.43
 ```
 
 ```python
@@ -89,7 +90,7 @@ Create a Python 3.9 environment and install gwaslab using pip:
 ```
 conda env create -n gwaslab_test -c conda-forge python=3.9
 conda activate gwaslab
-pip install gwaslab==3.4.41
+pip install gwaslab==3.4.43
 ```
 
 or create a new environment using yml file [environment_3.4.40.yml](https://github.com/Cloufield/gwaslab/blob/main/environment_3.4.40.yml)
@@ -193,6 +194,7 @@ dependencies:
       - adjustText==0.8
       - pysam==0.19
       - pyensembl==2.2.3
+      - h5py==3.10.0
 ```
 
 ## How to cite

{gwaslab-3.4.42.dist-info → gwaslab-3.4.44.dist-info}/RECORD

@@ -3,17 +3,18 @@ gwaslab/bd_common_data.py,sha256=v98X3tdRNOVE2gCiSHkfyBb0pSIjTk5IFG8A725Oj3o,126
 gwaslab/bd_config.py,sha256=TP-r-DPhJD3XnRYZbw9bQHXaDIkiRgK8bG9HCt-UaLc,580
 gwaslab/bd_download.py,sha256=cDDk2C5IvjeAzvPvVYGTkI4Ss33DUtEDjGo8eAbQRvY,15663
 gwaslab/bd_get_hapmap3.py,sha256=asNjQYeGfQi8u3jnfenRvDdKMs5ptql5wpcUzqMlwUI,3937
+gwaslab/cache_manager.py,sha256=HOTnSkCOyGEPLRl90WT8D_6pAdI8d8AzenMIDGuCeWc,28113
 gwaslab/g_Log.py,sha256=C3Zv-_6c3C9ms8bgQ-ytplz22sjk7euqXYkWr9zNeAs,1573
 gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gwaslab/g_Sumstats.py,sha256=GS0YUdvNYlwiR-mu6VJIv_JRqgBpHmTq9123XX5kiMI,35132
+gwaslab/g_Sumstats.py,sha256=NOEQd00guGch_GIt5bHv1wcrAvETfChqzmtgm-nIx_I,35298
 gwaslab/g_SumstatsPair.py,sha256=tbgT-_1CqDEw22s4LbVJWF3ChELxz0gy1DEBzLc9ODU,8833
 gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
 gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
 gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
 gwaslab/g_vchange_status.py,sha256=eX0jdIb6Spa07ZdpWNqUWqdVBWS0fuH2yrt4PDi3Res,1746
-gwaslab/g_version.py,sha256=sYIrfQwAxGSUHOGcP64nhQ71-Cgzax3Xs18GM0Os_9k,1818
+gwaslab/g_version.py,sha256=44qNMttuGuAyDPPblc1z0V9R5lHo9z8x2_E6JuZ6eBE,1818
 gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
-gwaslab/hm_harmonize_sumstats.py,sha256=n6aygO8V7MJaDgkNHozNzIsm_G8KcR70ukS-IOygw0E,67684
+gwaslab/hm_harmonize_sumstats.py,sha256=CADIG_KLsoq4y21wN0fyaaG2S4PDpKu96Y0of6b0TaU,78184
 gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
 gwaslab/io_preformat_input.py,sha256=w62JLAr16Ru0EgUtBCEV2eXRO89OqhidQxwf2IPAM38,20014
 gwaslab/io_read_ldsc.py,sha256=8S9n4imgl4d0WPms_GYld-6uUM5z7iWGiCA-M814kzY,12123
@@ -27,7 +28,7 @@ gwaslab/ldsc_parse.py,sha256=MBnfgcWlV4oHp9MoDRh1mpilaHhAR15Af77hMFn4-5k,10564
 gwaslab/ldsc_regressions.py,sha256=yzbGjgNV7u-SWXNPsh9S8y9mK97Bim_Nmad9G9V18ZU,30078
 gwaslab/ldsc_sumstats.py,sha256=O0olsDxKlh1MJ1gAuEN1t40rxhajOEwOQ20ak7xoDrI,26245
 gwaslab/qc_check_datatype.py,sha256=kW68uk4dTLOU2b1dHoVat6n0loundDysAjIqxsXW28Q,3379
-gwaslab/qc_fix_sumstats.py,sha256=Dp2HnVnqdO5aiXpLhnLsvL6XCKuC4Du2HJFEVIH2Ss0,87342
+gwaslab/qc_fix_sumstats.py,sha256=cpJibJ_77p4cg39R4zRunhOK2deIK4PfQA9wmYZgyqk,92745
 gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gwaslab/util_ex_calculate_ldmatrix.py,sha256=LpE__LoYRHLgVKlCHo6lYWlz9LEUVUDqYPEAP-Svbm0,14598
 gwaslab/util_ex_calculate_prs.py,sha256=5l1eiZs8YwIpEgp7i3IurP8n5KwQM5awbG9fWSm4iT4,9053
@@ -58,7 +59,7 @@ gwaslab/viz_plot_compare_effect.py,sha256=8om3y6YQfnOk4FfkKSpKr2KqJcsMeCwQ6FRRKb
 gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
 gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
 gwaslab/viz_plot_miamiplot2.py,sha256=SWv82D8UBbREKsk8EoKth-2w68l6FbXyVLsb_E1hh8o,15882
-gwaslab/viz_plot_mqqplot.py,sha256=xIx-m8IP0GAAKuIoiAbzxl3fkUDEEunczo6dVEZ3KRY,61671
+gwaslab/viz_plot_mqqplot.py,sha256=PzRWnm11whxww7ut-bzFkj1sbPc_c0OP7yRpIgYo2iQ,61739
 gwaslab/viz_plot_qqplot.py,sha256=psQgVpP29686CEZkzQz0iRbApzqy7aE3GGiBcazVvNw,7247
 gwaslab/viz_plot_regionalplot.py,sha256=PBIWkNj2fj-dRLKQJNpM8wor5jya2anqix0-UYLE0Is,37901
 gwaslab/viz_plot_rg_heatmap.py,sha256=PidUsgOiEVt6MfBPCF3_yDhOEytZ-I1q-ZD6_0pFrV4,13713
@@ -72,9 +73,9 @@ gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz,sha256=qD9RsC5S2h6l-OdpW
 gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz,sha256=Y8ZT2FIAhbhlgCJdE9qQVAiwnV_fcsPt72usBa7RSBM,10225828
 gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz,sha256=R7IkssKu0L4WwkU9SrS84xCMdrkkKL0gnTNO_OKbG0Y,219
 gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz,sha256=76CIU0pibDJ72Y6UY-TbIKE9gEPwTELAaIbCXyjm80Q,470
-gwaslab-3.4.42.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gwaslab-3.4.42.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.4.42.dist-info/METADATA,sha256=iqArSw_x7yXovyF9D-z3gt5fzskQSOVObXPWCrYIcsg,7714
-gwaslab-3.4.42.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-gwaslab-3.4.42.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.4.42.dist-info/RECORD,,
+gwaslab-3.4.44.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gwaslab-3.4.44.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.4.44.dist-info/METADATA,sha256=PJUO56s9S_nfVnZlRCYuSq-6BADrRxjcwjAqaAjJWc8,7764
+gwaslab-3.4.44.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+gwaslab-3.4.44.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.4.44.dist-info/RECORD,,