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
class ProtocolFormatterTest(unittest.TestCase):
maxDiff = None
json = """
{
"info": {
"name": "Test Protocol",
"author": "Michelle Steigerwalt",
"description": "A protocol to test JSON output.",
"created": "Thu Aug 11 20:19:55 2016",
"updated": ""
},
"instruments": {
"p10_a": {
"axis": "A",
"name": "p10"
},
"p200_b": {
"axis": "B",
"name": "p200"
}
},
"containers": [
{
"name": "microplate.96",
"label": "Ingredients",
"slot": "A1"
},
{
"name": "microplate.96",
"label": "Output",
"slot": "B1"
}
],
"instructions": [
{
"command": "transfer",
"start": "Ingredients:A1",
"end": "Output:B1",
"volume": 10,
"tool": "p10",
"blowout": true,
"touchtip": true
},
{
"command": "transfer_group",
"tool": "p10",
"transfers": [
{
"start": "Ingredients:A3",
"end": "Output:B3",
"volume": 3,
"blowout": true,
"touchtip": true
},
{
"start": "Ingredients:A4",
"end": "Output:B4",
"volume": 10,
"blowout": true,
"touchtip": true
},
{
"start": "Ingredients:A5",
"end": "Output:C1",
"volume": 10,
"blowout": true,
"touchtip": true
}
]
},
{
"command": "consolidate",
"tool": "p10",
"end": "Output:B3",
"transfers": [
{
"start": "Ingredients:A3",
"volume": 3,
"blowout": true,
"touchtip": true
},
{
"start": "Ingredients:A4",
"volume": 10,
"blowout": true,
"touchtip": true
},
{
"start": "Ingredients:A5",
"volume": 10,
"blowout": true,
"touchtip": true
}
]
},
{
"command": "distribute",
"tool": "p10",
"start": "Ingredients:A1",
"transfers": [
{
"end": "Output:A1",
"volume": 3,
"blowout": true,
"touchtip": true
},
{
"end": "Output:A2",
"volume": 10,
"blowout": true,
"touchtip": true
},
{
"end": "Output:A3",
"volume": 10,
"blowout": true,
"touchtip": true
}
]
},
{
"command": "mix",
"start": "Output:A1",
"volume": 50,
"tool": "p200",
"repetitions": 30,
"blowout": true,
"touchtip": true
}
]
}
"""
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 test_json_export(self):
result = json.loads(self.protocol.export(JSONFormatter))
expected = json.loads(self.json)
self.assertEqual(self.protocol.version, '0.0.1')
for k, v in self.stub_info.items():
self.assertEqual(v, result['info'][k])
self.assertEqual(result["info"]["version"], self.protocol.version)
self.assertEqual(result["info"]["version_hash"], self.protocol.hash)
expected['info'] = ""
result['info'] = ""
self.assertEqual(expected, result)
def test_invalid_json(self):
with self.assertRaises(x.ContainerMissing):
# This fails because there's no tiprack or trash.
self.protocol.export(JSONFormatter, validate_run=True)
def test_load_json(self):
start = self.json
f = JSONLoader(self.json)
dump = f.protocol.export(JSONFormatter)
result = json.loads(dump)
expected = json.loads(start)
expected['info'] = ""
result['info'] = ""
self.assertEqual(expected, result) # ✨ OMG isomorphic! ✨
def test_equal_hashing(self):
p = JSONLoader(self.json).protocol
# Hashes of all protocol run-related data within the JSON and manually
# defined protcol are equal.
self.assertEqual(self.protocol, p)
# Make a modification of the original protocol.
p.add_instrument('B', 'p20')
# Hashes are different.
self.assertNotEqual(self.protocol, p)
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