slidingWindow optimization

tahiri-lab · Nov 8, 2023 · f1c00cd · f1c00cd
1 parent 88877fd
commit f1c00cd
Showing 1 changed file with 7 additions and 6 deletions.
diff --git a/aphylogeo/alignement.py b/aphylogeo/alignement.py
@@ -757,15 +757,16 @@ def slidingWindow(self):
         for i in range(0, seq_len, step):
             if i + step < seq_len:
                 windowed_alignment[f"{i}_{i + step - 1}"] = {key: val[i : i + step - 1] for key, val in paddedMSA.items()}
-                combinations = itertools.combinations(windowed_alignment[f"{i}_{i + step - 1}"].values(),2)   
+                combinations = itertools.combinations(windowed_alignment[f"{i}_{i + step - 1}"].values(),2) 
+                df = pd.DataFrame(list(combinations))
+                if self.rate_similarity[0] < self.similarity(df):
+                    windowed_alignment.pop(f"{i}_{i + step - 1}")
             else:
                 windowed_alignment[f"{i}_{seq_len-1}"] = {key: val[i : i + seq_len - 1] for key, val in paddedMSA.items()}
                 combinations = itertools.combinations(windowed_alignment[f"{i}_{seq_len-1}"].values(),2)
-            df = pd.DataFrame(list(combinations))
-
-            #if self.rate_similarity[0] < self.similarity(df):
-            #    windowed_alignment.pop(f"{i}_{seq_len-1}")
-            #    print(self.rate_similarity)
+                df = pd.DataFrame(list(combinations))
+                if self.rate_similarity[0] < self.similarity(df):
+                    windowed_alignment.pop(f"{i}_{seq_len-1}")
 
         # JUST TO MAKE THE DEBUG FILES
         if self.makeDebugFiles: