gwaslab 3.4.44__tar.gz → 3.4.45__tar.gz

{gwaslab-3.4.44/src/gwaslab.egg-info → gwaslab-3.4.45}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.44
+Version: 3.4.45
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -8,7 +8,7 @@ Project-URL: Github, https://github.com/Cloufield/gwaslab
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: <=3.10,>=3.9
+Requires-Python: <3.11,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: LICENSE_before_v3.4.39
@@ -17,7 +17,7 @@ Requires-Dist: numpy>=1.21.2
 Requires-Dist: matplotlib!=3.7.2,>=3.5
 Requires-Dist: seaborn>=0.12
 Requires-Dist: scipy>=1.12
-Requires-Dist: pySAM<0.20,>=0.18.1
+Requires-Dist: pySAM==0.22.1
 Requires-Dist: Biopython>=1.79
 Requires-Dist: adjustText<=0.8,>=0.7.3
 Requires-Dist: liftover>=1.1.13

{gwaslab-3.4.44 → gwaslab-3.4.45}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.4.44"
+version = "3.4.45"
 authors = [
   { name="Yunye", email="yunye@gwaslab.com" },
 ]
@@ -21,7 +21,7 @@ dependencies = [
     "matplotlib>=3.5,!=3.7.2",
     "seaborn>=0.12",
     "scipy>=1.12",
-    "pySAM>=0.18.1,<0.20",
+    "pySAM==0.22.1",
     "Biopython>=1.79",
     "adjustText>=0.7.3, <=0.8",
     "liftover>=1.1.13",
@@ -31,7 +31,7 @@ dependencies = [
     "h5py>=3.10.0"
 ]
 
-requires-python = ">=3.9,<=3.10"
+requires-python = ">=3.9,<3.11"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",

{gwaslab-3.4.44 → gwaslab-3.4.45}/src/gwaslab/g_SumstatsPair.py

@@ -139,7 +139,7 @@ class SumstatsPair( ):
         self.clumps["clumps"], self.clumps["plink_log"] = _clump(self.data, log=self.log, p="P_1",mlog10p="MLOG10P_1", study = self.study_name, **kwargs)
 
     def to_coloc(self,**kwargs):
-        self.to_finemapping_file_path, self.plink_log = tofinemapping(self.data,study=self.study_name,suffixes=self.suffixes,log=self.log,**kwargs)
+        self.to_finemapping_file_path, output_file_list, self.plink_log = tofinemapping(self.data,study=self.study_name,suffixes=self.suffixes,log=self.log,**kwargs)
 
     def run_coloc_susie(self,**kwargs):
 

{gwaslab-3.4.44 → gwaslab-3.4.45}/src/gwaslab/g_vchange_status.py

@@ -1,13 +1,15 @@
 import pandas as pd
 
+CATEGORIES = {str(j+i) for j in [1900000,3800000,9700000,9800000,9900000] for i in range(0,100000)}
+
 def vchange_status(status,digit,before,after):
     dic={}
     for i in range(len(before)):
         dic[before[i]]=after[i]
     if digit>1:
-        return status.str[:digit-1]+status.str[digit-1].replace(dic)+status.str[digit:]
+        return pd.Categorical(status.str[:digit-1]+status.str[digit-1].replace(dic)+status.str[digit:],categories=CATEGORIES)
     else:
-        return status.str[digit-1].replace(dic)+status.str[digit:]
+        return pd.Categorical(status.str[digit-1].replace(dic)+status.str[digit:],categories=CATEGORIES)
 
 def copy_status(from_status,to_status, digit):
     if digit>1:

{gwaslab-3.4.44 → gwaslab-3.4.45}/src/gwaslab/g_version.py

@@ -15,8 +15,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.4.44",
-   "release_date":"20240424"
+   "version":"3.4.45",
+   "release_date":"20240509"
     }
     return dic   
 

{gwaslab-3.4.44 → gwaslab-3.4.45}/src/gwaslab/hm_harmonize_sumstats.py

@@ -355,7 +355,11 @@ def oldcheckref(sumstats,ref_seq,chrom="CHR",pos="POS",ea="EA",nea="NEA",status=
     
     log.write("\n",end="",show_time=False,verbose=verbose) 
         
-    sumstats[status] = sumstats[status].astype("string")
+    CATEGORIES = {str(j+i) for j in [1900000,3800000,9700000,9800000,9900000] for i in range(0,100000)}
+    sumstats[status] = pd.Categorical(sumstats[status],categories=CATEGORIES)
+    #sumstats[status] = sumstats[status].astype("string")
+
+
     available_to_check =sum( (~sumstats[pos].isna()) & (~sumstats[nea].isna()) & (~sumstats[ea].isna()))
     status_0=sum(sumstats["STATUS"].str.match("\w\w\w\w\w[0]\w", case=False, flags=0, na=False))
     status_3=sum(sumstats["STATUS"].str.match("\w\w\w\w\w[3]\w", case=False, flags=0, na=False))
@@ -669,9 +673,11 @@ def checkref(sumstats,ref_seq,chrom="CHR",pos="POS",ea="EA",nea="NEA",status="ST
         sumstats_to_check = sumstats.loc[to_check_ref,[chrom,pos,ea,nea,status]]
         sumstats.loc[to_check_ref,status] = check_status(sumstats_to_check, all_records_dict, log=log, verbose=verbose)
         log.write(" -Finished checking records", verbose=verbose) 
- 
-    sumstats[status] = sumstats[status].astype("string")
-        
+    
+    CATEGORIES = {str(j+i) for j in [1900000,3800000,9700000,9800000,9900000] for i in range(0,100000)}
+    sumstats[status] = pd.Categorical(sumstats[status],categories=CATEGORIES)
+    #sumstats[status] = sumstats[status].astype("string")
+
     available_to_check =sum( (~sumstats[pos].isna()) & (~sumstats[nea].isna()) & (~sumstats[ea].isna()))
     status_0=sum(sumstats["STATUS"].str.match("\w\w\w\w\w[0]\w", case=False, flags=0, na=False))
     status_3=sum(sumstats["STATUS"].str.match("\w\w\w\w\w[3]\w", case=False, flags=0, na=False))
@@ -700,6 +706,7 @@ def checkref(sumstats,ref_seq,chrom="CHR",pos="POS",ea="EA",nea="NEA",status="ST
     if remove is True:
         sumstats = sumstats.loc[~sumstats["STATUS"].str.match("\w\w\w\w\w[8]\w"),:]
         log.write(" -Variants not on given reference sequence were removed.",verbose=verbose)
+
     
     finished(log, verbose, _end_line)
     return sumstats

{gwaslab-3.4.44 → gwaslab-3.4.45/src/gwaslab.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.44
+Version: 3.4.45
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -8,7 +8,7 @@ Project-URL: Github, https://github.com/Cloufield/gwaslab
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: <=3.10,>=3.9
+Requires-Python: <3.11,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: LICENSE_before_v3.4.39
@@ -17,7 +17,7 @@ Requires-Dist: numpy>=1.21.2
 Requires-Dist: matplotlib!=3.7.2,>=3.5
 Requires-Dist: seaborn>=0.12
 Requires-Dist: scipy>=1.12
-Requires-Dist: pySAM<0.20,>=0.18.1
+Requires-Dist: pySAM==0.22.1
 Requires-Dist: Biopython>=1.79
 Requires-Dist: adjustText<=0.8,>=0.7.3
 Requires-Dist: liftover>=1.1.13

{gwaslab-3.4.44 → gwaslab-3.4.45}/src/gwaslab.egg-info/requires.txt

@@ -3,7 +3,7 @@ numpy>=1.21.2
 matplotlib!=3.7.2,>=3.5
 seaborn>=0.12
 scipy>=1.12
-pySAM<0.20,>=0.18.1
+pySAM==0.22.1
 Biopython>=1.79
 adjustText<=0.8,>=0.7.3
 liftover>=1.1.13