pairwise2: Convert substitution array to dict in dictionary_match (#3865

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biopython · Feb 15, 2022 · 4d37d81 · 4d37d81
1 parent 93c44bd
commit 4d37d81
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/Bio/pairwise2.py b/Bio/pairwise2.py
@@ -273,6 +273,7 @@
 
 from Bio import BiopythonWarning
 from Bio import BiopythonDeprecationWarning
+from Bio.Align import substitution_matrices
 
 warnings.warn(
     "Bio.pairwise2 has been deprecated, and we intend to remove it in a "
@@ -1282,6 +1283,8 @@ class dictionary_match:
 
     def __init__(self, score_dict, symmetric=1):
         """Initialize the class."""
+        if isinstance(score_dict, substitution_matrices.Array):
+            score_dict = dict(score_dict)  # Access to dict is much faster
         self.score_dict = score_dict
         self.symmetric = symmetric