Update mutation_analysis.py

mutation_analysis.py

@@ -1,16 +1,26 @@
 # mutation_analysis.py
 
-def classify_mutation(wt_protein: str, mut_protein: str) -> str:
+STOP_CODONS = {"UAA", "UAG", "UGA"}
+
+def classify_mutation(wt_protein: str, mutant_protein: str) -> str:
     """
-    Classify mutation based on protein sequences.
+    依照正確的分子生物學邏輯分類突變型態
     """
-    if wt_protein == mut_protein:
-        return "synonymous mutation"
 
-    if "*" in mut_protein:
-        return "nonsense mutation (premature stop codon)"
+    # 1️⃣ Nonsense mutation：出現提前終止
+    # （翻譯後蛋白中出現 STOP 或明顯提前終止）
+    if len(mutant_protein) < len(wt_protein):
+        # 若是「提前終止」但 reading frame 未被打亂 → nonsense
+        return "nonsense mutation"
 
-    if len(mut_protein) != len(wt_protein):
+    # 2️⃣ Frameshift mutation：reading frame 改變
+    # （長度變化且非單一替換）
+    if len(mutant_protein) != len(wt_protein):
         return "frameshift mutation"
 
-    return "missense mutation"
+    # 3️⃣ Missense mutation：長度相同但胺基酸不同
+    if wt_protein != mutant_protein:
+        return "missense mutation"
+
+    # 4️⃣ 沒有變化
+    return "no mutation"