Merge pull request #474 from groutr/str_replace

Use str.replace in make_gaps_ambiguous
nextstrain · Mar 25, 2020 · d2398eb · d2398eb
2 parents d47c9d7 + abdc038
commit d2398eb
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/augur/align.py b/augur/align.py
@@ -267,10 +267,10 @@ def make_gaps_ambiguous(aln):
         Biopython Alignment
     '''
     for seq in aln:
-        seq_array = np.array(seq)
-        gaps = seq_array=='-'
-        seq_array[gaps]='N'
-        seq.seq = Seq.Seq("".join(seq_array))
+        _seq = str(seq.seq)
+        _seq = _seq.replace('-', 'N')
+        seq.seq = Seq.Seq(_seq, alphabet=seq.seq.alphabet)
+
 
 def check_duplicates(*values):
     names = set()