feat: add annotations for bicodon CAI

Cauch-BS · Nov 11, 2024 · 41946cd · 41946cd
1 parent 27334a1
commit 41946cd
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diff --git a/vaxpress/scoring/aup.py b/vaxpress/scoring/aup.py
@@ -104,5 +104,6 @@ def annotate_sequence(self, seq, folding):
 
     def evaluate_local(self, seq, folding):
         xi_array = 1 - folding["pi_array"]
+        # moving average of xi_array
         baseindex = list(range(len(seq)))
         return {"aup": (baseindex, xi_array)}
diff --git a/vaxpress/scoring/bicodon.py b/vaxpress/scoring/bicodon.py
@@ -86,3 +86,10 @@ def score(self, seqs):
         bcai_score = bcai * self.weight
 
         return {"bicodon": bcai_score}, {"bicodon": bcai}
+
+    def evaluate_local(self, seq):
+        scores = self.bicodon_scores
+        seq = Sequence(seq).cdsseq
+        bcai = np.array([scores[seq[i : i + 6]] for i in range(0, len(seq) - 3, 3)])
+        centers = np.arange(0, len(seq) - 3, 3)
+        return {"bcai": (centers, bcai)}