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])
def test_eco_cutting(self):
"""Test basic cutting with EcoRI."""
self.assertEqual(EcoRI.site, 'GAATTC')
self.assertFalse(EcoRI.is_blunt())
self.assertTrue(EcoRI.is_5overhang())
self.assertFalse(EcoRI.is_3overhang())
self.assertEqual(EcoRI.elucidate(), "G^AATT_C")
self.assertEqual(EcoRI.search(self.ecosite_seq), [6])
parts = EcoRI.catalyse(self.ecosite_seq)
self.assertEqual(len(parts), 2)
self.assertEqual(str(parts[1]), "AATTCAAAA")
parts = EcoRI.catalyze(self.ecosite_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])
def test_eco_cutting(self):
"""Test basic cutting with EcoRI (5'overhang)."""
self.assertEqual(EcoRI.site, 'GAATTC')
self.assertTrue(EcoRI.cut_once())
self.assertFalse(EcoRI.is_blunt())
self.assertTrue(EcoRI.is_5overhang())
self.assertFalse(EcoRI.is_3overhang())
self.assertEqual(EcoRI.overhang(), "5' overhang")
self.assertTrue(EcoRI.is_defined())
self.assertFalse(EcoRI.is_ambiguous())
self.assertFalse(EcoRI.is_unknown())
self.assertTrue(EcoRI.is_palindromic())
self.assertTrue(EcoRI.is_comm())
self.assertIn('Life Technologies', EcoRI.supplier_list())
self.assertEqual(EcoRI.elucidate(), "G^AATT_C")
self.assertEqual(EcoRI.search(self.ecosite_seq), [6])
self.assertEqual(EcoRI.characteristic(), (1, -1, None, None, 'GAATTC'))
parts = EcoRI.catalyse(self.ecosite_seq)
self.assertEqual(len(parts), 2)
self.assertEqual(str(parts[1]), "AATTCAAAA")
parts = EcoRI.catalyze(self.ecosite_seq)
self.assertEqual(len(parts), 2)
def test_eco_cutting(self):
"""Test basic cutting with EcoRI (5'overhang)."""
self.assertEqual(EcoRI.site, 'GAATTC')
self.assertTrue(EcoRI.cut_once())
self.assertFalse(EcoRI.is_blunt())
self.assertTrue(EcoRI.is_5overhang())
self.assertFalse(EcoRI.is_3overhang())
self.assertEqual(EcoRI.overhang(), "5' overhang")
self.assertTrue(EcoRI.is_defined())
self.assertFalse(EcoRI.is_ambiguous())
self.assertFalse(EcoRI.is_unknown())
self.assertTrue(EcoRI.is_palindromic())
self.assertTrue(EcoRI.is_comm())
self.assertIn('Life Technologies', EcoRI.supplier_list())
self.assertEqual(EcoRI.elucidate(), "G^AATT_C")
self.assertEqual(EcoRI.search(self.ecosite_seq), [6])
self.assertEqual(EcoRI.characteristic(), (1, -1, None, None, 'GAATTC'))
parts = EcoRI.catalyse(self.ecosite_seq)
self.assertEqual(len(parts), 2)
self.assertEqual(str(parts[1]), "AATTCAAAA")
parts = EcoRI.catalyze(self.ecosite_seq)
self.assertEqual(len(parts), 2)