Update database.py

gnomad_db/database.py

@@ -9,10 +9,13 @@
 
 class gnomAD_DB:
 
-    def __init__(self, genodb_path, parallel=True, cpu_count=512):
+    def __init__(self, genodb_path, parallel=False, cpu_count=None):
+
 
-        self.cpu_count = min(cpu_count, int(multiprocessing.cpu_count()))
         self.parallel = parallel
+
+        if self.parallel:
+            self.cpu_count = cpu_count if isinstance(cpu_count, int) else int(multiprocessing.cpu_count())
 
         self.db_file = os.path.join(genodb_path, 'gnomad_db.sqlite3')
 
@@ -137,7 +140,7 @@ def get_maf_from_df(self, var_df: pd.DataFrame, query: str="AF") -> pd.Series:
         if self.parallel and len(var_df) > 100 * self.cpu_count:
             out = np.array_split(var_df, self.cpu_count)
             assert len(out) == self.cpu_count
-            out = Parallel(self.cpu_count)(delayed(self._get_maf_from_df)(df, query) for df in out)
+            out = Parallel(self.cpu_count, prefer="threads")(delayed(self._get_maf_from_df)(df, query) for df in out)
             out = pd.concat(out)
             out.set_index(var_df.index, inplace=True)
             assert len(var_df) == len(out)
@@ -204,4 +207,4 @@ def download_and_unzip(url, output_path):
         """
         download database and unzip file
         """
-        utils.download_and_unzip_file(url, output_path)
+        utils.download_and_unzip_file(url, output_path)