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])