def _assign(self, root):
"""Traverse tree and align sequences"""
if root.getValue()[2] == None:
if root.getLeft().getValue()[2] == None:
self._assign(root.getLeft())
if root.getRight().getValue()[2] == None:
self._assign(root.getRight())
# Get sequences
seq1 = root.getLeft().getValue()[2][1]
seq2 = root.getRight().getValue()[2][1]
(a1, a2, e1, e2, score, gaps) = \
align.NeedlemanWunsch(seq1, seq2, self.smx, 0, 0)
v1 = root.getLeft().getValue()
v2 = root.getRight().getValue()
nv1 = (v1[0], v1[1], v1[2], e1)
nv2 = (v2[0], v2[1], v2[2], e2)
root.getLeft().setValue(nv1)
root.getRight().setValue(nv2)
# Choose the sequence with least gaps
if e1 < e2:
nseq = a1
else:
nseq = a2
v1 = root.getValue()
nseq = (v1[0], nseq)
nv1 = (v1[0], v1[1], nseq, v1[3])
root.setValue(nv1)
import align str1 = [8, 0, 247, 166, 75, 130, 0, 1] str2 = [8, 0, 167, 210, 75, 130, 0, 12] (nseq1, nseq2, edits1, edits2, score, gaps) = align.NeedlemanWunsch(str1, str2, None, 0, 0) print nseq1 print nseq2
def test_NeedlemanWunsch():
# Test 1
print("Test 1:")
s1 = "CCC"
s2 = "CCC"
S = readScoringMatrix("DNA1.txt")
score, a1, a2 = align.NeedlemanWunsch(s1, s2, S, 1)
test_alignment(a1, a2, s1, s2, score, 3, S, 1)
print("Passed\n")
# Test 2
print("Test 2:")
s1 = "CCC"
s2 = "CTC"
S = readScoringMatrix("DNA1.txt")
score, a1, a2 = align.NeedlemanWunsch(s1, s2, S, 1)
test_alignment(a1, a2, s1, s2, score, 2, S, 1)
print("Passed\n")
# Test 3
print("Test 3:")
s1 = "CTC"
s2 = "CCC"
S = readScoringMatrix("DNA1.txt")
score, a1, a2 = align.NeedlemanWunsch(s1, s2, S, 1)
test_alignment(a1, a2, s1, s2, score, 2, S, 1)
print("Passed\n")
# Test 4
print("Test 4:")
s1 = "CCC"
s2 = "CC"
S = readScoringMatrix("DNA1.txt")
score, a1, a2 = align.NeedlemanWunsch(s1, s2, S, 1)
test_alignment(a1, a2, s1, s2, score, 1, S, 1)
print("Passed\n")
# Test 5
print("Test 5:")
s1 = "CC"
s2 = "CCC"
S = readScoringMatrix("DNA1.txt")
score, a1, a2 = align.NeedlemanWunsch(s1, s2, S, 1)
test_alignment(a1, a2, s1, s2, score, 1, S, 1)
print("Passed\n")
# Test 6
print("Test 6:")
s1 = "AGTA"
s2 = "ACA"
S = readScoringMatrix("DNA2.txt")
score, a1, a2 = align.NeedlemanWunsch(s1, s2, S, 2)
test_alignment(a1, a2, s1, s2, score, 7, S, 2)
print("Passed\n")
# Test 7
print("Test 7:")
s1 = "ACA"
s2 = "AGTA"
S = readScoringMatrix("DNA2.txt")
score, a1, a2 = align.NeedlemanWunsch(s1, s2, S, 2)
test_alignment(a1, a2, s1, s2, score, 7, S, 2)
print("Passed\n")
# Test 8
print("Test 8:")
s1 = "WWWGGWWW"
s2 = "WWWLWWW"
S = readScoringMatrix("Blosum62.txt")
score, a1, a2 = align.NeedlemanWunsch(s1, s2, S, 2)
test_alignment(a1, a2, s1, s2, score, 60, S, 2)
print("Passed\n")