def test_creating_batch(self):
"""Creating and modifying a restriction batch.
"""
batch = RestrictionBatch([EcoRI])
batch.add(KpnI)
batch += EcoRV
self.assertEqual(len(batch), 3)
# The usual way to test batch membership
self.assertIn(EcoRV, batch)
self.assertIn(EcoRI, batch)
self.assertIn(KpnI, batch)
self.assertNotIn(SmaI, batch)
# Syntax sugar for the above
self.assertIn('EcoRV', batch)
self.assertNotIn('SmaI', batch)
batch.get(EcoRV)
self.assertRaises(ValueError, batch.get, SmaI)
batch.remove(EcoRV)
self.assertEqual(len(batch), 2)
self.assertNotIn(EcoRV, batch)
self.assertNotIn('EcoRV', batch)
def test_creating_batch(self):
"""Creating and modifying a restriction batch."""
batch = RestrictionBatch([EcoRI])
batch.add(KpnI)
batch += EcoRV
self.assertEqual(len(batch), 3)
# The usual way to test batch membership
self.assertIn(EcoRV, batch)
self.assertIn(EcoRI, batch)
self.assertIn(KpnI, batch)
self.assertNotIn(SmaI, batch)
# Syntax sugar for the above
self.assertIn('EcoRV', batch)
self.assertNotIn('SmaI', batch)
batch.get(EcoRV)
self.assertRaises(ValueError, batch.get, SmaI)
batch.remove(EcoRV)
self.assertEqual(len(batch), 2)
self.assertNotIn(EcoRV, batch)
self.assertNotIn('EcoRV', batch)
# Create a batch with suppliers and other supplier related methods
# These tests may be 'update sensitive' since company names and
# products may change often...
batch = RestrictionBatch((), ('S')) # Sigma
self.assertEqual(batch.current_suppliers(),
['Sigma Chemical Corporation'])
self.assertIn(EcoRI, batch)
self.assertNotIn(AanI, batch)
batch.add_supplier('B') # Life Technologies
self.assertIn(AanI, batch)
def test_creating_batch(self):
"""Creating and modifying a restriction batch."""
batch = RestrictionBatch()
self.assertEqual(batch.suppl_codes()['N'], 'New England Biolabs')
self.assertTrue(batch.is_restriction(EcoRI))
batch = RestrictionBatch([EcoRI])
batch.add(KpnI)
batch += EcoRV
self.assertEqual(len(batch), 3)
self.assertEqual(batch.elements(), ['EcoRI', 'EcoRV', 'KpnI'])
# Problem with Python 3, as sequence of list may be different:
# self.assertEqual(batch.as_string(), ['EcoRI', 'KpnI', 'EcoRV'])
self.assertIn('EcoRI', batch.as_string())
# The usual way to test batch membership
self.assertIn(EcoRV, batch)
self.assertIn(EcoRI, batch)
self.assertIn(KpnI, batch)
self.assertNotIn(SmaI, batch)
# Syntax sugar for the above
self.assertIn('EcoRV', batch)
self.assertNotIn('SmaI', batch)
batch.get(EcoRV)
self.assertRaises(ValueError, batch.get, SmaI)
batch.get(SmaI, add=True)
self.assertEqual(len(batch), 4)
batch.remove(SmaI)
batch.remove(EcoRV)
self.assertEqual(len(batch), 2)
self.assertNotIn(EcoRV, batch)
self.assertNotIn('EcoRV', batch)
# Creating a batch by addition of restriction enzymes
new_batch = EcoRI + KpnI
self.assertEqual(batch, new_batch)
# or by addition of a batch with an enzyme
another_new_batch = new_batch + EcoRV
new_batch += EcoRV
self.assertEqual(another_new_batch, new_batch)
self.assertRaises(TypeError, EcoRI.__add__, 1)
# Create a batch with suppliers and other supplier related methods
# These tests may be 'update sensitive' since company names and
# products may change often...
batch = RestrictionBatch((), ('S')) # Sigma
self.assertEqual(batch.current_suppliers(),
['Sigma Chemical Corporation'])
self.assertIn(EcoRI, batch)
self.assertNotIn(AanI, batch)
batch.add_supplier('B') # Life Technologies
self.assertIn(AanI, batch)
def test_creating_batch(self):
"""Creating and modifying a restriction batch."""
batch = RestrictionBatch()
self.assertEqual(batch.suppl_codes()['N'], 'New England Biolabs')
self.assertTrue(batch.is_restriction(EcoRI))
batch = RestrictionBatch([EcoRI])
batch.add(KpnI)
batch += EcoRV
self.assertEqual(len(batch), 3)
self.assertEqual(batch.elements(), ['EcoRI', 'EcoRV', 'KpnI'])
# Problem with Python 3, as sequence of list may be different:
# self.assertEqual(batch.as_string(), ['EcoRI', 'KpnI', 'EcoRV'])
self.assertIn('EcoRI', batch.as_string())
# The usual way to test batch membership
self.assertIn(EcoRV, batch)
self.assertIn(EcoRI, batch)
self.assertIn(KpnI, batch)
self.assertNotIn(SmaI, batch)
# Syntax sugar for the above
self.assertIn('EcoRV', batch)
self.assertNotIn('SmaI', batch)
batch.get(EcoRV)
self.assertRaises(ValueError, batch.get, SmaI)
batch.get(SmaI, add=True)
self.assertEqual(len(batch), 4)
batch.remove(SmaI)
batch.remove(EcoRV)
self.assertEqual(len(batch), 2)
self.assertNotIn(EcoRV, batch)
self.assertNotIn('EcoRV', batch)
# Creating a batch by addition of restriction enzymes
new_batch = EcoRI + KpnI
self.assertEqual(batch, new_batch)
# or by addition of a batch with an enzyme
another_new_batch = new_batch + EcoRV
new_batch += EcoRV
self.assertEqual(another_new_batch, new_batch)
self.assertRaises(TypeError, EcoRI.__add__, 1)
# Create a batch with suppliers and other supplier related methods
# These tests may be 'update sensitive' since company names and
# products may change often...
batch = RestrictionBatch((), ('S')) # Sigma
self.assertEqual(batch.current_suppliers(),
['Sigma Chemical Corporation'])
self.assertIn(EcoRI, batch)
self.assertNotIn(AanI, batch)
batch.add_supplier('B') # Life Technologies
self.assertIn(AanI, batch)
def apply_restricts(dna, restricts, circular=False):
'''Applies restriction site cleavage to forward and reverse strands.'''
out_dnas = [dna]
for restrict in restricts:
batch = RestrictionBatch()
batch.add(str(restrict))
restrict = batch.get(str(restrict))
out_dnas = _apply_restrict_to_dnas(out_dnas, restrict, circular)
return out_dnas