Added comparison with ref + fixed in-place return

alignementseq.py

@@ -11,6 +11,8 @@ import Bio.SeqIO
 from Bio.SeqRecord import SeqRecord
 from Bio.Seq import Seq
 
+import Bio.pairwise2
+
 seqs=[]
 handle = open("balibase/RV11.unaligned/BBS11001.fasta")
 for seq in Bio.SeqIO.parse(handle, "fasta"):
@@ -219,9 +221,11 @@ def align2steps(seq1, seq2, d=8, e=4):
         j -=1
     alx = alx[::-1]
     aly = aly[::-1]
-    seq1.seq = Seq(alx)
-    seq2.seq = Seq(aly)
-    return bestScore, seq1, seq2
+    aseq1 = SeqRecord(seq1)
+    aseq1.seq = Seq(alx)
+    aseq2 = SeqRecord(seq2)
+    aseq2.seq = Seq(aly)
+    return bestScore, aseq1, aseq2
 
 def test():
 #    print(align("chat", "cat"))
@@ -233,4 +237,13 @@ def test():
     print(y.seq)
     with open("balibase/us/1.fasta", "w") as fd:
         Bio.SeqIO.write((x, y), fd, "fasta")
+    print("Ref:")
+    ref = Bio.pairwise2.align.globalds(
+            seqs[0].seq, seqs[1].seq,
+            Bio.SubsMat.MatrixInfo.blosum62, -8, -4)
+        
+    for x, y, s, *_ in ref:
+        print(s)
+        print(x)
+        print(y)
 test()