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])
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_comparisons(self):
"""Test comparison operators between different enzymes."""
# Comparison of iso- and neoschizomers
self.assertEqual(Acc65I, Acc65I)
self.assertNotEqual(Acc65I, KpnI)
self.assertFalse(Acc65I == Asp718I)
# self.assertNotEqual(Acc65I, Asp718I) it doesn't work as expected
self.assertFalse(Acc65I != Asp718I)
self.assertNotEqual(Acc65I, EcoRI)
self.assertTrue(Acc65I >> KpnI)
self.assertFalse(Acc65I >> Asp718I)
# Compare length of recognition sites
self.assertFalse(EcoRI >= EcoRV)
self.assertTrue(EcoRV >= EcoRI)
with self.assertRaises(NotImplementedError):
EcoRV >= 3
self.assertFalse(EcoRI > EcoRV)
self.assertTrue(EcoRV > EcoRI)
with self.assertRaises(NotImplementedError):
EcoRV > 3
self.assertTrue(EcoRI <= EcoRV)
self.assertFalse(EcoRV <= EcoRI)
with self.assertRaises(NotImplementedError):
EcoRV <= 3
self.assertTrue(EcoRI < EcoRV)
self.assertFalse(EcoRV < EcoRI)
with self.assertRaises(NotImplementedError):
EcoRV < 3
# Compare compatible overhangs
self.assertTrue(Acc65I % Asp718I)
self.assertTrue(Acc65I % Acc65I)
self.assertFalse(Acc65I % KpnI)
with self.assertRaises(TypeError):
Acc65I % "KpnI"
self.assertTrue(SmaI % EcoRV)
self.assertTrue(EarI % EarI)
self.assertIn(EcoRV, SmaI.compatible_end())
self.assertIn(Acc65I, Asp718I.compatible_end())
def test_comparisons(self):
"""Test comparison operators between different enzymes."""
# Comparison of iso- and neoschizomers
self.assertEqual(Acc65I, Acc65I)
self.assertNotEqual(Acc65I, KpnI)
self.assertFalse(Acc65I == Asp718I)
self.assertFalse(Acc65I != Asp718I)
self.assertNotEqual(Acc65I, EcoRI)
self.assertTrue(Acc65I >> KpnI)
self.assertFalse(Acc65I >> Asp718I)
# Compare length of recognition sites
self.assertFalse(EcoRI >= EcoRV)
self.assertTrue(EcoRV >= EcoRI)
with self.assertRaises(NotImplementedError):
EcoRV >= 3
self.assertFalse(EcoRI > EcoRV)
self.assertTrue(EcoRV > EcoRI)
with self.assertRaises(NotImplementedError):
EcoRV > 3
self.assertTrue(EcoRI <= EcoRV)
self.assertFalse(EcoRV <= EcoRI)
with self.assertRaises(NotImplementedError):
EcoRV <= 3
self.assertTrue(EcoRI < EcoRV)
self.assertFalse(EcoRV < EcoRI)
with self.assertRaises(NotImplementedError):
EcoRV < 3
# Compare compatible overhangs
self.assertTrue(Acc65I % Asp718I)
self.assertTrue(Acc65I % Acc65I)
self.assertFalse(Acc65I % KpnI)
with self.assertRaises(TypeError):
Acc65I % 'KpnI'
self.assertTrue(SmaI % EcoRV)
self.assertTrue(EarI % EarI)
self.assertIn(EcoRV, SmaI.compatible_end())
self.assertIn(Acc65I, Asp718I.compatible_end())