def test_model_to_model(self):
"""Model sequence should convert to model sequence"""
r = RNA.make_array_seq("AAA", name="x")
s = RNA.make_array_seq(r)
self.assertEqual(str(s), "AAA")
self.assertEqual(s.moltype, RNA)
self.assertEqual(s.name, "x")
def test_regular_to_regular(self):
"""Regular sequence should convert to regular sequence"""
r = RNA.make_seq("AAA", name="x")
s = RNA.make_seq(r)
self.assertEqual(str(s), "AAA")
self.assertEqual(s.moltype, RNA)
self.assertEqual(s.name, "x")
def test_strand_symmetric_motifs(self):
"""construction of strand symmetric motif sets"""
# fails for a moltype with no strand complement
with self.assertRaises(TypeError):
PROTEIN.strand_symmetric_motifs()
got = DNA.strand_symmetric_motifs(motif_length=1)
expect = set([("A", "T"), ("C", "G")])
self.assertEqual(got, expect)
got = RNA.strand_symmetric_motifs(motif_length=1)
expect = set([("A", "U"), ("C", "G")])
self.assertEqual(got, expect)
got = DNA.strand_symmetric_motifs(motif_length=2)
self.assertEqual(len(got), 8)
got = DNA.strand_symmetric_motifs(motif_length=3)
self.assertEqual(len(got), 32)
