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_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 find_EcoRi (DNA_sequence):
"Find EcoRi restriction site and give position of sticky ends"
pos=[]
eco_start= EcoRI.search(DNA_sequence)
for entry in eco_start:
eco_end = entry + 4
pos.append(entry)
pos.append(eco_end)
return(pos);
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."""
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_sequence_object(self):
"""Test if sequence must be a Seq or MutableSeq object."""
with self.assertRaises(TypeError):
seq = FormattedSeq('GATC')
seq = FormattedSeq(Seq('TAGC'))
seq = FormattedSeq(MutableSeq('AGTC'))
seq = FormattedSeq(seq)
with self.assertRaises(TypeError):
EcoRI.search('GATC')
EcoRI.search(Seq('ATGC'))
EcoRI.search(MutableSeq('TCAG'))
def test_sequence_object(self):
"""Test if sequence must be a Seq or MutableSeq object."""
with self.assertRaises(TypeError):
seq = FormattedSeq('GATC')
seq = FormattedSeq(Seq('TAGC'))
seq = FormattedSeq(MutableSeq('AGTC'))
seq = FormattedSeq(seq)
with self.assertRaises(TypeError):
EcoRI.search('GATC')
EcoRI.search(Seq('ATGC'))
EcoRI.search(MutableSeq('TCAG'))
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)