gwaslab 3.6.4__tar.gz → 3.6.6__tar.gz

{gwaslab-3.6.4/src/gwaslab.egg-info → gwaslab-3.6.6}/PKG-INFO

@@ -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 → gwaslab-3.6.6}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.6.4"
+version = "3.6.6"
 authors = [
   { name="Yunye", email="gwaslab@gmail.com" },
 ]

{gwaslab-3.6.4 → gwaslab-3.6.6}/src/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-3.6.4 → gwaslab-3.6.6}/src/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-3.6.4 → gwaslab-3.6.6}/src/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-3.6.4 → gwaslab-3.6.6}/src/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 → gwaslab-3.6.6/src/gwaslab.egg-info}/PKG-INFO

@@ -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/