def test_N_special_treatment(self):
"""
i)A and N at pos 2 are different, but still consensus
ii)N and N at pos 0 are same, but not consensus"""
alignment = make_alignment(["NTN", "NTA"])
result = PrgBuilder.get_consensus(alignment)
self.assertEqual(result, "*TA")
def test_all_gap_nonmatch(self):
alignment = make_alignment(["A--A", "A--A"])
result = PrgBuilder.get_consensus(alignment)
self.assertEqual(result, "A**A")
def test_IUPACAmbiguous_nonmatch(self):
alignment = make_alignment(["RYA", "RTA"])
result = PrgBuilder.get_consensus(alignment)
self.assertEqual(result, "**A")
def test_mixed_match_nonmatch(self):
alignment = make_alignment(["AAGTA", "CATTA"])
result = PrgBuilder.get_consensus(alignment)
self.assertEqual(result, "*A*TA")