def test_basic_isochizomers(self):
"""Test to be sure isochizomer and neoschizomers are as expected.
"""
self.assertEqual(Acc65I.isoschizomers(), [Asp718I, KpnI])
self.assertEqual(Acc65I.elucidate(), 'G^GTAC_C')
self.assertEqual(Asp718I.elucidate(), 'G^GTAC_C')
self.assertEqual(KpnI.elucidate(), 'G_GTAC^C')
def test_basic_isochizomers(self):
"""Test to be sure isochizomer and neoschizomers are as expected."""
self.assertEqual(Acc65I.isoschizomers(), [Asp718I, KpnI])
self.assertEqual(Acc65I.elucidate(), 'G^GTAC_C')
self.assertEqual(Asp718I.elucidate(), 'G^GTAC_C')
self.assertEqual(KpnI.elucidate(), 'G_GTAC^C')
self.assertTrue(Acc65I.is_isoschizomer(KpnI))
self.assertFalse(Acc65I.is_equischizomer(KpnI))
self.assertTrue(Acc65I.is_neoschizomer(KpnI))
self.assertIn(Acc65I, Asp718I.equischizomers())
self.assertIn(KpnI, Asp718I.neoschizomers())
self.assertIn(KpnI, Acc65I.isoschizomers())
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_kpn_cutting(self):
"""Test basic cutting with KpnI (3'overhang)."""
self.assertTrue(KpnI.is_3overhang())
self.assertFalse(KpnI.is_5overhang())
self.assertFalse(KpnI.is_blunt())
self.assertEqual(KpnI.overhang(), "3' overhang")
parts = KpnI.catalyse(self.kpnsite_seq)
self.assertEqual(len(parts), 2)
self.assertEqual(KpnI.catalyse(self.kpnsite_seq),
KpnI.catalyze(self.kpnsite_seq))
def test_basic_isochizomers(self):
"""Test to be sure isochizomer and neoschizomers are as expected."""
self.assertEqual(Acc65I.isoschizomers(), [Asp718I, KpnI])
self.assertEqual(Acc65I.elucidate(), 'G^GTAC_C')
self.assertEqual(Asp718I.elucidate(), 'G^GTAC_C')
self.assertEqual(KpnI.elucidate(), 'G_GTAC^C')
self.assertTrue(Acc65I.is_isoschizomer(KpnI))
self.assertFalse(Acc65I.is_equischizomer(KpnI))
self.assertTrue(Acc65I.is_neoschizomer(KpnI))
self.assertIn(Acc65I, Asp718I.equischizomers())
self.assertIn(KpnI, Asp718I.neoschizomers())
self.assertIn(KpnI, Acc65I.isoschizomers())
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_kpn_cutting(self):
"""Test basic cutting with KpnI (3'overhang)."""
self.assertTrue(KpnI.is_3overhang())
self.assertFalse(KpnI.is_5overhang())
self.assertFalse(KpnI.is_blunt())
self.assertEqual(KpnI.overhang(), "3' overhang")
parts = KpnI.catalyse(self.kpnsite_seq)
self.assertEqual(len(parts), 2)
self.assertEqual(KpnI.catalyse(self.kpnsite_seq),
KpnI.catalyze(self.kpnsite_seq))