def test_ear_cutting(self):
"""Test basic cutting with EarI (ambiguous overhang)."""
self.assertFalse(EarI.is_palindromic())
self.assertFalse(EarI.is_defined())
self.assertTrue(EarI.is_ambiguous())
self.assertFalse(EarI.is_unknown())
self.assertEqual(EarI.elucidate(), 'CTCTTCN^NNN_N')
def test_ear_cutting(self):
"""Test basic cutting with EarI (ambiguous overhang)."""
self.assertFalse(EarI.is_palindromic())
self.assertFalse(EarI.is_defined())
self.assertTrue(EarI.is_ambiguous())
self.assertFalse(EarI.is_unknown())
self.assertEqual(EarI.elucidate(), 'CTCTTCN^NNN_N')
def test_cutting_border_positions(self):
"""Check if cutting after first and penultimate position works."""
# Use EarI, cuts as follows: CTCTTCN^NNN_N
seq = Seq('CTCTTCA')
self.assertEqual(EarI.search(seq), [])
seq += 'A'
self.assertEqual(EarI.search(seq), [8])
# Recognition site on reverse-complement strand
seq = Seq('AAAAGAAGAG')
self.assertEqual(EarI.search(seq), [])
seq = 'A' + seq
self.assertEqual(EarI.search(seq), [2])
def test_cutting_border_positions(self):
"""Check if cutting after first and penultimate position works."""
# Use EarI, cuts as follows: CTCTTCN^NNN_N
seq = Seq('CTCTTCA')
self.assertEqual(EarI.search(seq), [])
seq += 'A'
self.assertEqual(EarI.search(seq), [8])
# Recognition site on reverse-complement strand
seq = Seq('AAAAGAAGAG')
self.assertEqual(EarI.search(seq), [])
seq = 'A' + seq
self.assertEqual(EarI.search(seq), [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_recognition_site_on_both_strands(self):
"""Check if recognition sites on both strands are properly handled."""
seq = Seq('CTCTTCGAAGAG')
self.assertEqual(EarI.search(seq), [3, 8])
def test_recognition_site_on_both_strands(self):
"""Check if recognition sites on both strands are properly handled."""
seq = Seq('CTCTTCGAAGAG')
self.assertEqual(EarI.search(seq), [3, 8])