Here are the examples of the python api autoprotocol.protocol.Protocol taken from open source projects. By voting up you can indicate which examples are most useful and appropriate.
10 Examples
0
Example 1
Project: transcriptic Source File: AP2En_test.py
def test_web_example(self):
p = Protocol()
bacterial_sample = p.ref("bacteria", None, "micro-1.5", discard=True)
test_plate = p.ref("test_plate", None, "96-flat", storage="cold_4")
p.dispense_full_plate(test_plate, "lb-broth-noAB", "50:microliter")
w = 0
amt = 1
while amt < 20:
p.transfer(bacterial_sample.well(
0), test_plate.well(w), "%d:microliter" % amt)
amt += 2
w += 1
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(forest, [[1], [2], [3], [4], [5], [
6], [7], [8], [9], [10], [11]])
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Example 2
Project: transcriptic Source File: AP2En_test.py
def test_measure_suite(self):
"""
Desired Output:
1. Measure concentration of 2.0 microliters DNA source aliquots
2. Measure mass of test_plate2
3. Measure volume of 12 wells from test_plate
4. Measure volume of 8 wells from test_plate2
"""
p = Protocol()
test_plate = p.ref("test_plate", None, "96-flat", storage="cold_4")
test_plate2 = p.ref("test_plate2", id=None,
cont_type="96-flat", storage=None, discard=True)
for well in test_plate2.all_wells():
well.set_volume("150:microliter")
p.measure_concentration(wells=test_plate2.wells_from(
0, 96), dataref="mc_test", measurement="DNA", volume=Unit(2, "microliter"))
p.measure_mass(test_plate2, "test_ref")
p.measure_volume(test_plate.wells_from(0, 12), "test_ref")
p.measure_volume(test_plate2.wells_from(1, 8), "test_ref2")
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output, ["Measure concentration of 2.0 microliters DNA source aliquots of test_plate2",
"Measure mass of test_plate2",
"Measure volume of 12 wells from test_plate",
"Measure volume of 8 wells from test_plate2"])
self.assertEqual(forest, [[1, [2, [4]]], [3]])
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Example 3
Project: transcriptic Source File: AP2En_test.py
def test_mag_incubate(self):
"""
Desired Output:
1. Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0
2. Distribute from test/1 into wells test/7, test/8, test/9
3. Distribute from test/2 into wells test/10
4. Distribute from test/0 into wells test/1
5. Magnetically incubate pcr_0 for 30.0 minutes with a tip position of 1.5
"""
p = Protocol()
pcrs = [p.ref("pcr_%s" % i, None, "96-pcr", storage="cold_20")
for i in range(7)]
pcr = pcrs[0]
p.mag_release("96-pcr", pcr, "30:second", "1:hertz",
center=float(5) / 100, amplitude=0)
c = p.ref("test", None, "96-flat", discard=True)
srcs = c.wells_from(1, 2).set_volume("100:microliter")
dests = c.wells_from(7, 4)
p.distribute(srcs, dests, "30:microliter", allow_carryover=True)
p.distribute(c.well("A1").set_volume(
"20:microliter"), c.well("A2"), "5:microliter")
p.mag_incubate("96-pcr", pcr, "30:minute",
temperature="30:celsius")
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output, ["Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0",
"Distribute from test/1 into wells test/7, test/8, test/9",
"Distribute from test/2 into wells test/10",
"Distribute from test/0 into wells test/1",
"Magnetically incubate pcr_0 for 30.0 minutes with a tip position of 1.5"])
self.assertEqual(forest, [[1, [5]], [2, [4]], [3]])
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Example 4
Project: transcriptic Source File: AP2En_test.py
def test_mag_mix(self):
"""
Desired Output:
1. Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0
2. Distribute from test/1 into wells test/7, test/8, test/9
3. Distribute from test/2 into wells test/10
4. Distribute from test/0 into wells test/1
5. Magnetically mix pcr_0 beads for 30.0 seconds at an amplitude of 0
"""
p = Protocol()
pcrs = [p.ref("pcr_%s" % i, None, "96-pcr", storage="cold_20")
for i in range(7)]
pcr = pcrs[0]
p.mag_release("96-pcr", pcr, "30:second", "1:hertz",
center=float(5) / 100, amplitude=0)
c = p.ref("test", None, "96-flat", discard=True)
srcs = c.wells_from(1, 2).set_volume("100:microliter")
dests = c.wells_from(7, 4)
p.distribute(srcs, dests, "30:microliter", allow_carryover=True)
p.distribute(c.well("A1").set_volume(
"20:microliter"), c.well("A2"), "5:microliter")
p.mag_mix("96-pcr", pcr, "30:second", "60:hertz",
center=float(100) / 100, amplitude=0)
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output, ["Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0",
"Distribute from test/1 into wells test/7, test/8, test/9",
"Distribute from test/2 into wells test/10",
"Distribute from test/0 into wells test/1",
"Magnetically mix pcr_0 beads for 30.0 seconds at an amplitude of 0"])
self.assertEqual(forest, [[1, [5]], [2, [4]], [3]])
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Example 5
Project: transcriptic Source File: AP2En_test.py
def test_mag_dry(self):
"""
Desired Output:
1. Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0
2. Distribute from test/1 into wells test/7, test/8, test/9
3. Distribute from test/2 into wells test/10
4. Distribute from test/0 into wells test/1
5. Magnetically dry pcr_0 for 30.0 minutes
"""
p = Protocol()
pcrs = [p.ref("pcr_%s" % i, None, "96-pcr", storage="cold_20")
for i in range(7)]
pcr = pcrs[0]
p.mag_release("96-pcr", pcr, "30:second", "1:hertz",
center=float(5) / 100, amplitude=0)
c = p.ref("test", None, "96-flat", discard=True)
srcs = c.wells_from(1, 2).set_volume("100:microliter")
dests = c.wells_from(7, 4)
p.distribute(srcs, dests, "30:microliter", allow_carryover=True)
p.distribute(c.well("A1").set_volume(
"20:microliter"), c.well("A2"), "5:microliter")
p.mag_dry("96-pcr", pcr, "30:minute",
new_tip=False, new_instruction=False)
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output, ["Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0",
"Distribute from test/1 into wells test/7, test/8, test/9",
"Distribute from test/2 into wells test/10",
"Distribute from test/0 into wells test/1",
"Magnetically dry pcr_0 for 30.0 minutes"])
self.assertEqual(forest, [[1, [5]], [2, [4]], [3]])
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Example 6
Project: transcriptic Source File: AP2En_test.py
def test_mag_collect(self):
"""
Desired Output:
1. Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0
2. Distribute from test/1 into wells test/7, test/8, test/9
3. Distribute from test/2 into wells test/10
4. Distribute from test/0 into wells test/1
5. Magnetically collect pcr_0 beads for 5 cycles with a pause duration of 30.0 seconds
"""
p = Protocol()
pcrs = [p.ref("pcr_%s" % i, None, "96-pcr", storage="cold_20")
for i in range(7)]
pcr = pcrs[0]
p.mag_release("96-pcr", pcr, "30:second", "1:hertz",
center=float(5) / 100, amplitude=0)
c = p.ref("test", None, "96-flat", discard=True)
srcs = c.wells_from(1, 2).set_volume("100:microliter")
dests = c.wells_from(7, 4)
p.distribute(srcs, dests, "30:microliter", allow_carryover=True)
p.distribute(c.well("A1").set_volume(
"20:microliter"), c.well("A2"), "5:microliter")
p.mag_collect("96-pcr", pcr, 5, "30:second",
bottom_position=float(5) / 100)
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output, ["Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0",
"Distribute from test/1 into wells test/7, test/8, test/9",
"Distribute from test/2 into wells test/10",
"Distribute from test/0 into wells test/1",
"Magnetically collect pcr_0 beads for 5 cycles with a pause duration of 30.0 seconds"])
self.assertEqual(forest, [[1, [5]], [2, [4]], [3]])
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Example 7
Project: transcriptic Source File: AP2En_test.py
def test_purify(self):
"""
Desired Output:
1. Perform gel purification on the 0.8% agarose gel with band range(s) 0-10
2. Perform gel purification on the 0.8% agarose gel with band range(s) 0-10
3. Perform gel purification on the 0.8% agarose gel with band range(s) 0-10
"""
p = Protocol()
sample_wells = p.ref("sample_wells", None, "96-pcr",
discard=True).wells_from(0, 20)
extract_wells = [p.ref("extract_%s" % i, None, "micro-1.5",
storage="cold_4").well(0) for i in sample_wells]
extract = [
{
"source": sample_wells[i],
"band_list": [{
"band_size_range": {"min_bp": 0, "max_bp": 10},
"elution_volume": Unit("5:microliter"),
"elution_buffer": "water",
"destination": d
}],
"lane": None,
"gel": None
} for i, d in enumerate(extract_wells)
]
p.gel_purify(extract, "10:microliter",
"size_select(8,0.8%)", "ladder1", "gel_purify_test")
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output, ["Perform gel purification on the 0.8% agarose gel with band range(s) 0-10",
"Perform gel purification on the 0.8% agarose gel with band range(s) 0-10",
"Perform gel purification on the 0.8% agarose gel with band range(s) 0-10"])
self.assertEqual(forest, [[1, [2, [3]]]])
0
Example 8
Project: transcriptic Source File: AP2En_test.py
def test_dispense_suite(self):
"""
Desired Output:
1. Dispense 100 microliters of water to the full plate of sample_plate5
2. Dispense corresponding amounts of water to 12 column(s) of sample_plate5
3. Dispense 50 microliters of reagent with resource ID rs17gmh5wafm5p to the full plate of sample_plate5
"""
p = Protocol()
sample_plate5 = p.ref("sample_plate5", None,
"96-flat", storage="warm_37")
p.dispense_full_plate(sample_plate5, "water", "100:microliter")
p.dispense(sample_plate5,
"water",
[{"column": 0, "volume": "10:microliter"},
{"column": 1, "volume": "20:microliter"},
{"column": 2, "volume": "30:microliter"},
{"column": 3, "volume": "40:microliter"},
{"column": 4, "volume": "50:microliter"},
{"column": 5, "volume": "60:microliter"},
{"column": 6, "volume": "70:microliter"},
{"column": 7, "volume": "80:microliter"},
{"column": 8, "volume": "90:microliter"},
{"column": 9, "volume": "100:microliter"},
{"column": 10, "volume": "110:microliter"},
{"column": 11, "volume": "120:microliter"}
])
p.dispense_full_plate(sample_plate5, "rs17gmh5wafm5p", "50:microliter", is_resource_id=True)
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
forest = parser_instance.forest_list
self.assertEqual(
parsed_output, ["Dispense 100 microliters of water to the full plate of sample_plate5",
"Dispense corresponding amounts of water to 12 column(s) of sample_plate5",
"Dispense 50 microliters of resource with resource ID rs17gmh5wafm5p to the full plate of sample_plate5"])
self.assertEqual(forest, [[1, [2, [3]]]])
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Example 9
Project: transcriptic Source File: AP2En_test.py
def test_illumina(self):
"""
Desired Output:
1. Illumina sequence wells test_plate6/0, test_plate6/1 with library size 34
"""
p = Protocol()
sample_wells6 = p.ref(
"test_plate6", None, "96-pcr", discard=True).wells_from(0, 8)
p.illuminaseq("PE", [{"object": sample_wells6[0], "library_concentration": 1.0},
{"object": sample_wells6[1], "library_concentration": 2}],
"nextseq", "mid", 'none', 34, "dataref")
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output, ["Illumina sequence wells test_plate6/0, test_plate6/1 with library size 34"])
self.assertEqual(forest, [[1]])
0
Example 10
Project: transcriptic Source File: AP2En_test.py
def test_flow(self):
"""
Desired Output:
1. Perform flow cytometry on well0 with the respective FSC and SSC channel parameters
"""
p = Protocol()
dataref = "test_ref"
well0 = p.ref("test_plate", None, "96-pcr",
discard=True).well(0)
FSC = {"voltage_range": {"low": "230:volt", "high": "280:volt"},
"area": True, "height": True, "weight": False}
SSC = {"voltage_range": {"low": "230:volt", "high": "280:volt"},
"area": True, "height": True, "weight": False}
channel0 = [FSC, SSC]
neg_controls = [{"well": well0, "volume": "100:microliter",
"captured_events": 5, "channel": channel0}]
samples = [{"well": well0,
"volume": "100:microliter", "captured_events": 9}]
p.flow_analyze(dataref, FSC, SSC, neg_controls,
samples)
pjsonString = json.dumps(p.as_dict(), indent=2)
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output, ["Perform flow cytometry on test_plate/0 with the respective FSC and SSC channel parameters"])
self.assertEqual(forest, [[1]])