fdr type check and logging

hgb-bin-proteomics · Jan 11, 2024 · 9e3a7fc · 9e3a7fc
1 parent e6848a9
commit 9e3a7fc
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/msannika_fdr.py b/msannika_fdr.py
@@ -195,6 +195,9 @@ def main(argv = None) -> List[pd.DataFrame]:
                         version = __version)
     args = parser.parse_args(argv)
 
+    if args.fdr is not None:
+        print(f"Using {float(args.fdr) if float(args.fdr) < 1.0 else float(args.fdr) / 100.0} FDR.")
+
     result_list = list()
 
     for f, file in enumerate(args.files):
@@ -205,10 +208,10 @@ def main(argv = None) -> List[pd.DataFrame]:
             crosslinks.to_excel(file.rstrip(".xlsx") + "_crosslinks.xlsx", sheet_name = "Crosslinks", index = False)
             result_list.append(crosslinks)
             if args.fdr is not None:
-                validated_csms = MSAnnika_CSM_Validator.validate(df, args.fdr if args.fdr < 1.0 else args.fdr / 100)
+                validated_csms = MSAnnika_CSM_Validator.validate(df, float(args.fdr) if float(args.fdr) < 1.0 else float(args.fdr) / 100.0)
                 validated_csms.to_excel(file.rstrip(".xlsx") + "_validated.xlsx", sheet_name = "CSMs", index = False)
                 result_list.append(validated_csms)
-                validated_crosslinks = MSAnnika_Crosslink_Validator.validate(crosslinks, args.fdr if args.fdr < 1.0 else args.fdr / 100)
+                validated_crosslinks = MSAnnika_Crosslink_Validator.validate(crosslinks, float(args.fdr) if float(args.fdr) < 1.0 else float(args.fdr) / 100.0)
                 validated_crosslinks.to_excel(file.rstrip(".xlsx") + "_crosslinks_validated.xlsx", sheet_name = "Crosslinks", index = False)
                 result_list.append(validated_crosslinks)
         else: