gwaslab 3.6.4__py3-none-any.whl → 3.6.6__py3-none-any.whl

gwaslab/g_version.py

@@ -17,8 +17,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.6.4",
-   "release_date":"20250624"
+   "version":"3.6.6",
+   "release_date":"20250704"
     }
     return dic   
 

gwaslab/io_read_pipcs.py

@@ -11,7 +11,8 @@ def _read_pipcs(data,
                 group=None,
                 studie_names=None,
                 log=Log(),
-                verbose=True):
+                verbose=True,
+                **readcsv_kwargs):
     
     log.write("Start to load PIP and CREDIBLE_SET_INDEX from file...",verbose=verbose)
     log.write(" -File:{}".format(output_prefix),verbose=verbose)
@@ -32,14 +33,14 @@ def _read_pipcs(data,
         pipcs_single_list=[]
         for index,pipcs_path in enumerate(pipcs_path_list):
             log.write(" -Loading {}:".format(pipcs_loci_list[index]) + pipcs_path)
-            pipcs_single = pd.read_csv(pipcs_path)
+            pipcs_single = pd.read_csv(pipcs_path,**readcsv_kwargs)
             if "LOCUS" not in pipcs_single.columns:
                 pipcs_single["LOCUS"]=pipcs_loci_list[index]
             pipcs_single_list.append(pipcs_single)
 
         pipcs = pd.concat(pipcs_single_list, axis=0, ignore_index=True) 
     else:
-        pipcs = pd.read_csv("{}".format(output_prefix))
+        pipcs = pd.read_csv("{}".format(output_prefix),**readcsv_kwargs)
     
     if "CHR" not in pipcs.columns:
         log.write(" -Merging CHR and POS from main dataframe...",verbose=verbose)

gwaslab/io_to_formats.py

@@ -402,11 +402,11 @@ def tofmt(sumstats,
     
 ####################################################################################################################
 def _write_tabular(sumstats,rename_dictionary, path, tab_fmt, to_csvargs, to_tabular_kwargs, log, verbose):
-    chr_header = rename_dictionary["CHR"]
     if tab_fmt=="tsv" or tab_fmt=="csv":
         try:
             log.write(f"  -Fast to csv mode...",verbose=verbose)
             if "@" in path:
+                chr_header = rename_dictionary["CHR"]
                 log.write(f"  -@ detected: writing each chromosome to a single file...",verbose=verbose)
                 log.write("  -Chromosomes:{}...".format(list(sumstats["CHR"].unique())),verbose=verbose)
                 for single_chr in list(sumstats["CHR"].unique()):
@@ -420,6 +420,7 @@ def _write_tabular(sumstats,rename_dictionary, path, tab_fmt, to_csvargs, to_tab
         except:
             log.write(f"Error in using fast_to_csv. Falling back to original implementation.",verbose=verbose)
             if "@" in path:
+                chr_header = rename_dictionary["CHR"]
                 log.write(f"  -@ detected: writing each chromosome to a single file...",verbose=verbose)
                 log.write("  -Chromosomes:{}...".format(list(sumstats["CHR"].unique())),verbose=verbose)
                 for single_chr in list(sumstats["CHR"].unique()):

gwaslab/viz_plot_miamiplot2.py

@@ -102,9 +102,16 @@ def plot_miami2(
             cols = ["CHR","POS","P"]
 
     if cols1 is None:
-        cols1 = cols.copy()
+        if scaled1 == True:
+            cols1 = ["CHR","POS","MLOG10P"]
+        else:
+            cols1 = ["CHR","POS","P"]
+    
     if cols2 is None:
-        cols2 = cols.copy()
+        if scaled2 == True:
+            cols2 = ["CHR","POS","MLOG10P"]
+        else:
+            cols2 = ["CHR","POS","P"]
 
     if id1 is not None:
         cols1.append(id1)
@@ -206,8 +213,15 @@ def plot_miami2(
         sumstats2 = merged_sumstats[cols2].copy()
 
     ## rename and quick fix ###########################################################################################################
-    renaming_dict1 = {cols1[0]:"CHR",cols1[1]:"POS",cols1[2]:"P"}
-    renaming_dict2 = {cols2[0]:"CHR",cols2[1]:"POS",cols2[2]:"P"}
+    if scaled1==True:
+        renaming_dict1 = {cols1[0]:"CHR",cols1[1]:"POS",cols1[2]:"MLOG10P"}
+    else:
+        renaming_dict1 = {cols1[0]:"CHR",cols1[1]:"POS",cols1[2]:"P"}
+    if scaled2==True:
+        renaming_dict2 = {cols2[0]:"CHR",cols2[1]:"POS",cols2[2]:"MLOG10P"}
+    else:
+        renaming_dict2 = {cols2[0]:"CHR",cols2[1]:"POS",cols2[2]:"P"}
+    
 
     sumstats1 = sumstats1.rename(columns=renaming_dict1)
     sumstats1 = _quick_fix(sumstats1,chr_dict=chr_dict1, scaled=scaled1, verbose=verbose, log=log)
@@ -292,6 +306,7 @@ def plot_miami2(
                       _chrom_df_for_i = chrom_df,
                       _invert=False,
                       _if_quick_qc=False,
+                      font_family=font_family,
                       **mqq_args1
                      )
     log.write("Finished creating Manhattan plot for sumstats1".format(_get_version()), verbose=verbose)
@@ -311,6 +326,7 @@ def plot_miami2(
                       _chrom_df_for_i = chrom_df,
                        _invert=True,
                       _if_quick_qc=False,
+                      font_family=font_family,
                      **mqq_args2)
     log.write("Finished creating Manhattan plot for sumstats2".format(_get_version()), verbose=verbose)
     

{gwaslab-3.6.4.dist-info → gwaslab-3.6.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.6.4
+Version: 3.6.6
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <gwaslab@gmail.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/

{gwaslab-3.6.4.dist-info → gwaslab-3.6.6.dist-info}/RECORD

@@ -18,7 +18,7 @@ gwaslab/g_meta.py,sha256=pXtSsQfFPv2UJmOxKMmLtcsp_Ku_H73YP7PnlfMd0sg,6472
 gwaslab/g_meta_update.py,sha256=dWgz4kcq9bvsXycCjfhoYtcJHlEP4HRdYoQ8KFqMyTQ,2490
 gwaslab/g_vchange_status.py,sha256=w3zsYYOcCaI3PTeboonvkQjudzUAfVIgATzRdiPViZs,1939
 gwaslab/g_vchange_status_polars.py,sha256=kxyGQCur0ibVFBCyZghA-XNf_kLDXKK-l7VC-Om2IdA,1839
-gwaslab/g_version.py,sha256=YdDG4Pd2xl9SjNiP8yq5slF3aQ4KCaQj83-AWW_edBk,1964
+gwaslab/g_version.py,sha256=O0RYviQ98EWaeYDgFXJmxW8qQ8nWSiuXxk7V9Ym8E-s,1964
 gwaslab/hm_casting.py,sha256=xoq1E4Tp5VC4aLWfq9-_AfiQzb1WZAHrnZG33W4sCOE,14178
 gwaslab/hm_casting_polars.py,sha256=CAPfCucj-ARtwP80EuHc9q2gLdj8TL_XQ7_sEC9LxA0,11440
 gwaslab/hm_harmonize_sumstats.py,sha256=2MeWnWmMHpLWjUMTVqExpg_3mE1VIaBsh6Mz3ffJCMc,84761
@@ -28,9 +28,9 @@ gwaslab/io_preformat_input.py,sha256=jIacIVymCfHVBlonUCFRmUJobLcxMWn2w_vWqXjESPg
 gwaslab/io_preformat_input_polars.py,sha256=HGdi6rXPQnYjTW8fMUds-uF6Lt8uElL3Er_Afv3OjTc,24767
 gwaslab/io_process_args.py,sha256=TIv0DyaVEcHnLBGdOD52GBZiO6nAQJycAmmVdEYPmRE,1918
 gwaslab/io_read_ldsc.py,sha256=9tV4AfQZmCAyiNSR9uALmXWOytWhBdT0pfMAY5Mx_QQ,13407
-gwaslab/io_read_pipcs.py,sha256=MPkdVDff_JTmoBCDswg_GO0UQ1tFas2rI0jLuMRqRjY,2891
+gwaslab/io_read_pipcs.py,sha256=w0UsP2lyGpYpNosw3LSI2zs54LTgDMizCQlePla4Vsc,2959
 gwaslab/io_read_tabular.py,sha256=EG-C6KhCutt4J4LlOMgXnqzJvU-EZXzVhMvaDFnHrMM,2380
-gwaslab/io_to_formats.py,sha256=uAmZ4xzVoJqXGXxwTZlbppli4fPc2EshnuTJm2DC4v8,32799
+gwaslab/io_to_formats.py,sha256=PlBarRW4QbDI2HE4RLSb4yA_xBjJapajeBPzQsYk8s8,32865
 gwaslab/io_to_pickle.py,sha256=HhePU0VcaGni0HTNU0BqoRaOnrr0NOxotgY6ISdx3Ck,1833
 gwaslab/ldsc_irwls.py,sha256=83JbAMAhD0KOfpv4IJa6LgUDfQjp4XSJveTjnhCBJYQ,6142
 gwaslab/ldsc_jackknife.py,sha256=XrWHoKS_Xn9StG1I83S2vUMTertsb-GH-_gOFYUhLeU,17715
@@ -94,7 +94,7 @@ gwaslab/viz_plot_credible_sets.py,sha256=RC5ZsuW8-0w0S1h4c--PZrYwfHfgZ3clM-9JcoM
 gwaslab/viz_plot_effect.py,sha256=qbM6c1IB2HlUlMNgFZlJ5G8ODQJ8-oSWD8t0Q8DDuz8,10653
 gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
 gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
-gwaslab/viz_plot_miamiplot2.py,sha256=5O4Ho8_FsSkBcunFVlbAkYuLAMxNqE6swLVtmvkoR6c,17495
+gwaslab/viz_plot_miamiplot2.py,sha256=thukuvia6dGexGcprYVyOt-M5iSCjbpqvMVfRrY6fgk,18015
 gwaslab/viz_plot_mqqplot.py,sha256=W0rKC8I0KrUvv5zakiTcPTEF_ttrUucrwoFS5MHLIyQ,71283
 gwaslab/viz_plot_phe_heatmap.py,sha256=qoXVeFTIm-n8IinNbDdPFVBSz2yGCGK6QzTstXv6aj4,9532
 gwaslab/viz_plot_qqplot.py,sha256=cB4vRlFv69zWY9NMLfSkfAbirYp3_EEW2kQiBTEMDoc,7483
@@ -112,9 +112,9 @@ 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-3.6.4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gwaslab-3.6.4.dist-info/licenses/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.6.4.dist-info/METADATA,sha256=0-B3gOWawfkr19AO_m-H8S-Mgtxe5o_yvCAGCJx59_Y,7073
-gwaslab-3.6.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-gwaslab-3.6.4.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.6.4.dist-info/RECORD,,
+gwaslab-3.6.6.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gwaslab-3.6.6.dist-info/licenses/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.6.6.dist-info/METADATA,sha256=QUXTQeaGhZ9x28IikmoJ5TIkABVj9AxbN4wfqnr9Ogw,7073
+gwaslab-3.6.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+gwaslab-3.6.6.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.6.6.dist-info/RECORD,,