def test_sma_cutting(self):
"""Test basic cutting with SmaI (blunt cutter)."""
self.assertTrue(SmaI.is_blunt())
self.assertFalse(SmaI.is_3overhang())
self.assertFalse(SmaI.is_5overhang())
self.assertEqual(SmaI.overhang(), 'blunt')
parts = SmaI.catalyse(self.smasite_seq)
self.assertEqual(len(parts), 2)
self.assertEqual(str(parts[1]), "GGGAAAA")
parts = SmaI.catalyze(self.smasite_seq)
self.assertEqual(len(parts), 2)
def test_sma_cutting(self):
"""Test basic cutting with SmaI (blunt cutter)."""
self.assertTrue(SmaI.is_blunt())
self.assertFalse(SmaI.is_3overhang())
self.assertFalse(SmaI.is_5overhang())
self.assertEqual(SmaI.overhang(), 'blunt')
parts = SmaI.catalyse(self.smasite_seq)
self.assertEqual(len(parts), 2)
self.assertEqual(str(parts[1]), "GGGAAAA")
parts = SmaI.catalyze(self.smasite_seq)
self.assertEqual(len(parts), 2)
def test_circular_sequences(self):
"""Deal with cutting circular sequences."""
parts = EcoRI.catalyse(self.ecosite_seq, linear=False)
self.assertEqual(len(parts), 1)
locations = EcoRI.search(parts[0], linear=False)
self.assertEqual(locations, [1])
parts = KpnI.catalyse(self.kpnsite_seq, linear=False)
self.assertEqual(len(parts), 1)
locations = KpnI.search(parts[0], linear=False)
self.assertEqual(locations, [1])
parts = SmaI.catalyse(self.smasite_seq, linear=False)
self.assertEqual(len(parts), 1)
locations = SmaI.search(parts[0], linear=False)
self.assertEqual(locations, [1])
self.assertEqual(
EarI.search(FormattedSeq(Seq('CTCTTCAAAAA')), linear=False), [8])
self.assertEqual(
SnaI.search(FormattedSeq(Seq('GTATACAAAAA')), linear=False), [1])
def test_circular_sequences(self):
"""Deal with cutting circular sequences."""
parts = EcoRI.catalyse(self.ecosite_seq, linear=False)
self.assertEqual(len(parts), 1)
locations = EcoRI.search(parts[0], linear=False)
self.assertEqual(locations, [1])
parts = KpnI.catalyse(self.kpnsite_seq, linear=False)
self.assertEqual(len(parts), 1)
locations = KpnI.search(parts[0], linear=False)
self.assertEqual(locations, [1])
parts = SmaI.catalyse(self.smasite_seq, linear=False)
self.assertEqual(len(parts), 1)
locations = SmaI.search(parts[0], linear=False)
self.assertEqual(locations, [1])
self.assertEqual(EarI.search(FormattedSeq(Seq('CTCTTCAAAAA')),
linear=False), [8])
self.assertEqual(SnaI.search(FormattedSeq(Seq('GTATACAAAAA')),
linear=False), [1])