Search in the serology mapping before looking at reduced list. Also cleanup

Author: pbashyal-nmdp

pyard/ard.py

@@ -260,14 +260,13 @@ def _redux_allele(
             # find serology equivalent in serology_mapping
             serology_mapping = db.find_serology_for_allele(self.db_connection, allele)
             serology_set = set()
-            if is_2_field_allele(allele):
+            for serology, allele_list in serology_mapping.items():
+                if allele in allele_list.split("/"):
+                    serology_set.add(serology)
+            if not serology_set and is_2_field_allele(allele):
                 for serology, allele_list in serology_mapping.items():
                     allele_list_lgx = self.redux(allele_list, "lgx")
-                    if allele in allele_list_lgx:
-                        serology_set.add(serology)
-            else:
-                for serology, allele_list in serology_mapping.items():
-                    if allele in allele_list:
+                    if allele in allele_list_lgx.split("/"):
                         serology_set.add(serology)
             return "/".join(
                 sorted(

pyard/load.py

@@ -153,7 +153,7 @@ def load_allele_list(imgt_version):
     :return: pandas Dataframe of Alleles
     """
 
-    # Create a Pandas DataFrame from the mac_code list file
+    # Create a Pandas DataFrame from the AlleleList file
     # Skip the header (first 6 lines) and use only the Allele column
     if imgt_version == "Latest":
         allele_list_url = f"{IMGT_HLA_URL}Latest/Allelelist.txt"

scripts/pyard

@@ -116,5 +116,4 @@ if __name__ == "__main__":
         sys.exit(2)
     else:
         # Remove ard and close db connection
-        print("Removing")
         del ard