def test_protocol_equality(self):
# Set up a protocol.
p1 = Protocol()
p1.add_instrument('A', 'p200')
p1.add_container('C1', 'tiprack.p200')
p1.add_container('A1', 'microplate.96')
p1.calibrate('A1', x=1, y=2, z=3)
p1.calibrate_instrument('A', top=0, blowout=10)
p1.transfer('A1:A1', 'A1:A2', ul=100)
p1.transfer('A1:A2', 'A1:A3', ul=80)
# And a copy.
p2 = Protocol()
p2.add_container('A1', 'microplate.96')
p2.add_container('C1', 'tiprack.p200')
p2.add_instrument('A', 'p200')
p2.calibrate('A1', x=1, y=2, z=3)
p2.calibrate_instrument('A', top=0, blowout=10)
p2.transfer('A1:A1', 'A1:A2', ul=100)
p2.transfer('A1:A2', 'A1:A3', ul=80)
# They're identical.
self.assertEqual(p1, p2)
# Make a change.
p2.add_instrument('B', 'p10')
# No longer identical.
self.assertNotEqual(p1, p2)
def test_protocol_addition_of_partials(self):
p1 = Protocol()
p1.add_instrument('A', 'p20')
p1.add_container('A1', 'microplate.96')
p1.transfer('A1:A1', 'A1:A2', ul=10)
p2 = Protocol.partial()
p2.add_container('A2', 'microplate.96')
p2.transfer('A1:A1', 'A1:A3', ul=20)
p2.transfer('A2:A1', 'A2:A4', ul=15)
p3 = Protocol.partial()
p3.add_container('A3', 'microplate.96')
p3.transfer('A1:A1', 'A1:A3', ul=20)
p3.transfer('A1:A1', 'A3:A4', ul=15)
p4 = Protocol()
p4.add_instrument('A', 'p20')
p4.add_container('A1', 'microplate.96')
p4.add_container('A2', 'microplate.96')
p4.add_container('A3', 'microplate.96')
p4.transfer('A1:A1', 'A1:A2', ul=10)
p4.transfer('A1:A1', 'A1:A3', ul=20)
p4.transfer('A2:A1', 'A2:A4', ul=15)
p4.transfer('A1:A1', 'A1:A3', ul=20)
p4.transfer('A1:A1', 'A3:A4', ul=15)
self.assertEqual(p4, p1 + p2 + p3)
def test_protocol_addition_container_conflict(self):
p1 = Protocol()
p1.add_instrument('A', 'p10')
p1.add_container('A1', 'microplate.96')
p1.transfer('A1:A1', 'A1:A2', ul=10)
p2 = Protocol()
p2.add_container('A1', 'tiprack.p20')
with self.assertRaises(x.ContainerConflict):
p1 + p2
def test_protocol_addition_info(self):
p1 = Protocol()
p1.set_info(author="John Doe", name="Lorem Ipsum")
p2 = Protocol()
p2.set_info(author="Jane Doe")
p3 = p1 + p2
self.assertEqual('Jane Doe', p3.info['author'])
self.assertEqual('Lorem Ipsum', p3.info['name'])
def test_protocol_addition_label_case(self):
p1 = Protocol()
p1.add_instrument('A', 'p10')
p1.add_container('A1', 'microplate.96', label="Input")
p2 = Protocol()
p2.add_instrument('A', 'p10')
p2.add_container('A1', 'microplate.96', label="INPUT")
p3 = Protocol()
p3.add_instrument('A', 'p10')
p3.add_container('A1', 'microplate.96', label="INPUT")
self.assertEqual((p1 + p2), p3)
def test_protocol_addition_label_conflict(self):
p1 = Protocol()
p1.add_instrument('A', 'p10')
p1.add_container('A1', 'microplate.96', label="Input")
p1.transfer('A1:A1', 'A1:A1', ul=10)
p2 = Protocol()
p2.add_instrument('A', 'p10') # Same definition; no conflict.
p2.add_instrument('B', 'p20') # New instrument.
p2.add_container('A1', 'microplate.96', label="Output") # Conflict.
p2.add_container('A2', 'microplate.96') # New container.
p2.transfer('A1:A1', 'A1:A1', ul=12)
p2.transfer('Output:A1', 'A2:A2', ul=20)
with self.assertRaises(x.ContainerConflict):
p1 + p2
def __init__(self, json_str):
data = json.loads(json_str)
self._protocol = Protocol()
self._load_info(data['info'])
self._load_containers(data['containers'])
self._load_instruments(data['instruments'])
self._load_instructions(data['instructions'])
def test_protocol_added_to_partial(self):
p1 = Protocol()
p1.add_instrument('A', 'p20')
p1.add_container('A1', 'microplate.96')
p1.transfer('A1:A1', 'A1:A2', ul=10)
p2 = Protocol.partial()
p2.add_container('A2', 'microplate.96')
p2.transfer('A1:A1', 'A1:A3', ul=20)
p2.transfer('A2:A1', 'A2:A4', ul=15)
with self.assertRaises(TypeError):
p2 + p1
def test_protocol_label_addition(self):
p1 = Protocol()
p1.add_instrument('A', 'p10')
p1.add_container('A1', 'microplate.96', label="Input")
p1.transfer('A1:A1', 'A1:A1', ul=10)
p2 = Protocol()
p2.add_instrument('A', 'p10') # Same definition; no conflict.
p2.add_instrument('B', 'p20') # New instrument.
p2.add_container('A1', 'microplate.96', label="Input") # No conflict.
p2.add_container('A2', 'microplate.96') # New container.
p2.transfer('A1:A1', 'A1:A1', ul=9)
p2.transfer('Input:A1', 'A2:A2', ul=20)
p3 = Protocol()
p3.add_instrument('A', 'p10')
p3.add_instrument('B', 'p20')
p3.add_container('A1', 'microplate.96', label="Input")
p3.add_container('A2', 'microplate.96')
p3.transfer('A1:A1', 'A1:A1', ul=10)
p3.transfer('A1:A1', 'A1:A1', ul=9)
p3.transfer('A1:A1', 'A2:A2', ul=20)
self.assertEqual(p3, p1 + p2)
def setUp(self):
self.protocol = Protocol()
self.stub_info = {
'name': "Test Protocol",
'description': "A protocol to test JSON output.",
'author': "Michelle Steigerwalt",
'created': "Thu Aug 11 20:19:55 2016"
}
# Same definitions as the protocol JSON above.
self.protocol.set_info(**self.stub_info)
self.protocol.add_instrument('A', 'p10')
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96', label="Ingredients")
self.protocol.add_container('B1', 'microplate.96', label="Output")
self.protocol.transfer('A1:A1', 'B1:B1', ul=10, tool='p10')
self.protocol.transfer_group(
('A1:A3', 'B1:B3', {'ul': 3}),
('INGREDIENTS:A4', 'B1:B4'),
('A1:A5', 'B1:C1'),
tool='p10',
ul=10
)
self.protocol.consolidate(
'Output:B3',
('A1:A3', {'ul': 3}),
'INGREDIENTS:A4',
'A1:A5',
tool='p10',
ul=10
)
self.protocol.distribute(
'Ingredients:A1',
('Output:A1', {'ul': 3}),
'Output:A2',
'Output:A3',
tool='p10',
ul=10
)
self.protocol.mix('Output:A1', ul=50, repetitions=30)
def setUp(self):
self.protocol = Protocol()
self.maxDiff = None
def setUp(self):
self.protocol = Protocol()
def __init__(self, protocol=None):
if protocol:
self._protocol = protocol
else:
self._protocol = Protocol()
def compile(*sequences, output=None):
"""
Takes a list of sequence arguments (RVD or DNA) and outputs a generated
protocol to make plasmids targetting those sequences.
"""
sequences = list(sequences)
# Limit right now is the number of tips in the static deck map we're
# using for this protocol.
if len(sequences) > 15:
raise ValueError("FusX compiler only supports up to 15 sequences.")
# Argument normalization.
normalized = []
for i, s in enumerate(sequences):
try:
normalized.append(_normalize_sequence(s))
except ValueError as e:
raise ValueError("Sequence #{}: {}".format(i + 1, e))
# Make the transfers for every sequence.
buffers = []
tals = []
enzymes = []
well_map = {}
for n, s in enumerate(normalized):
n = n + 1
if n > 12:
well = 'B{}'.format(n - 12)
else:
well = 'A{}'.format(n)
# We're going to do all the buffers at the start...
buffers += [('Ingredients:A1', 'FusX Output:' + well, 10)]
# TALs in the middle...
tals += _get_tal_transfers(s, well=well)
# Enzyme (BsmBI) at the end.
enzymes += [("Ingredients:B1", 'FusX Output:' + well, 10)]
# For printing an output map.
well_map[well] = sequences[n - 1] # Map to original input.
# Nicely formatted well map for the description.
output_map = []
for well in sorted(well_map):
output_map.append("{}: {}".format(well, well_map[well]))
protocol = Protocol()
protocol.set_info(name="FusX Transfer",
created=str(datetime.date.today()),
description="; ".join(output_map))
protocol.add_instrument('A', 'p10')
protocol.add_instrument('B', 'p200')
protocol.add_container('A1', 'tuberack.15-50ml', label='Ingredients')
protocol.add_container('E1', 'microplate.96', label='Fusx Output')
protocol.add_container('A2', 'point.trash')
protocol.add_container('E3', 'microplate.96') # Cool deck.
protocol.add_container('B2', 'tiprack.p10')
protocol.add_container('B1', 'tiprack.p10')
protocol.add_container('B3', 'tiprack.p10')
protocol.add_container('C1', 'microplate.96', label='TALE1')
protocol.add_container('D1', 'microplate.96', label='TALE2')
protocol.add_container('C2', 'microplate.96', label='TALE3')
protocol.add_container('D2', 'microplate.96', label='TALE4')
protocol.add_container('C3', 'microplate.96', label='TALE5')
# Take our three transfer groups and make them into a consolidated
# transfer list.
# Buffers
group = []
for start, end, volume in buffers:
group.append((start, end, {'ul': volume}))
protocol.transfer_group(*group, tool="p10")
# TALS
for start, end, volume in tals:
protocol.transfer(start, end, ul=volume)
# Enzymes
for start, end, volume in enzymes:
protocol.transfer(start, end, ul=volume)
compiled = protocol.export(JSONFormatter)
if output:
with open(output, 'w') as f:
f.write(compiled)
return compiled
