gwaslab 3.6.5__tar.gz → 3.6.6__tar.gz

{gwaslab-3.6.5/src/gwaslab.egg-info → gwaslab-3.6.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.6.5
+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-3.6.5 → gwaslab-3.6.6}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.6.5"
+version = "3.6.6"
 authors = [
   { name="Yunye", email="gwaslab@gmail.com" },
 ]

{gwaslab-3.6.5 → gwaslab-3.6.6}/src/gwaslab/g_version.py

@@ -17,8 +17,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.6.5",
-   "release_date":"20250625"
+   "version":"3.6.6",
+   "release_date":"20250704"
     }
     return dic   
 

{gwaslab-3.6.5 → 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-3.6.5 → 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-3.6.5 → gwaslab-3.6.6/src/gwaslab.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.6.5
+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/