def test_sna_cutting(self):
"""Test basic cutting with SnaI (unknown)."""
self.assertEqual(SnaI.elucidate(), '? GTATAC ?')
self.assertFalse(SnaI.is_defined())
self.assertFalse(SnaI.is_ambiguous())
self.assertTrue(SnaI.is_unknown())
self.assertFalse(SnaI.is_comm())
self.assertEqual(SnaI.suppliers(), None)
self.assertEqual(SnaI.supplier_list(), [])
with self.assertRaises(TypeError):
SnaI.buffers('no company')
def test_sna_cutting(self):
"""Test basic cutting with SnaI (unknown)."""
self.assertEqual(SnaI.elucidate(), '? GTATAC ?')
self.assertFalse(SnaI.is_defined())
self.assertFalse(SnaI.is_ambiguous())
self.assertTrue(SnaI.is_unknown())
self.assertFalse(SnaI.is_comm())
self.assertEqual(SnaI.suppliers(), None)
self.assertEqual(SnaI.supplier_list(), [])
with self.assertRaises(TypeError):
SnaI.buffers('no company')
def test_supplier(self):
"""Test output of supplier list for different enzyme types."""
out = self.StringIO()
self.sys.stdout = out
EcoRI.suppliers()
self.assertIn('Life Technologies', out.getvalue())
self.assertEqual(SnaI.suppliers(), None)
EcoRI.all_suppliers() # Independent of enzyme, list of all suppliers
self.assertIn('Agilent Technologies', out.getvalue())
batch = EcoRI + SnaI
batch.show_codes()
self.assertIn('N = New England Biolabs', out.getvalue())
self.sys.stdout = self.sys.__stdout__
def test_supplier(self):
"""Test output of supplier list for different enzyme types."""
out = self.StringIO()
self.sys.stdout = out
EcoRI.suppliers()
self.assertIn('Life Technologies', out.getvalue())
self.assertEqual(SnaI.suppliers(), None)
EcoRI.all_suppliers() # Independent of enzyme, list of all suppliers
self.assertIn('Agilent Technologies', out.getvalue())
batch = EcoRI + SnaI
batch.show_codes()
self.assertIn('N = New England Biolabs', out.getvalue())
self.sys.stdout = self.sys.__stdout__
def test_supplier(self):
"""Test output of supplier list for different enzyme types."""
out = self.StringIO()
self.sys.stdout = out
EcoRI.suppliers()
self.assertIn("Thermo Fisher Scientific", out.getvalue())
self.assertIsNone(SnaI.suppliers())
EcoRI.all_suppliers() # Independent of enzyme, list of all suppliers
self.assertIn("Agilent Technologies", out.getvalue())
batch = EcoRI + SnaI
batch.show_codes()
self.assertIn("N = New England Biolabs", out.getvalue())
self.sys.stdout = self.sys.__stdout__
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])