def test(self):
module = importlib.import_module(module_path)
f = open(self.temp_file_path,'wb')
f.write(json.dumps(inputs,indent=4))
f.close()
run(module.main,protocol_name, config=self.temp_file_path)
p.spin(container, '3000:g', '3:second')
p.mix(dna_wells)
if params.get('measure_concentration'):
p.measure_concentration(dna_wells, 'dna_concentration', 'DNA', ul(2))
if params.get('split_tubes'):
#create a separate container and take half to be used for other experiments
new_container = p.ref('%s_2' % container.name,
cont_type=container.container_type,
storage=Temperature.cold_4.name)
for dna_well in dna_wells:
new_dna_well = new_container.well(dna_well.index)
new_dna_well.name = dna_well.name
p.transfer(dna_well, new_dna_well, dna_well.volume / 2)
for property_name in PROPERTIES_TO_COPY:
if dna_well.properties.get(property_name):
set_property(new_dna_well, property_name,
dna_well.properties[property_name])
if __name__ == '__main__':
run(main, "DNAResuspension")
storage="cold_80",
cell_line_name=cell_line_name).well(0))
copy_cell_line_name(source_bacteria_well, cryo_vial_wells)
set_property(cryo_vial_wells, 'antibiotic', antibiotic.name)
p.distribute(mix_well2, cryo_vial_wells, ul(115), allow_carryover=True)
if destroy_source_tube:
source_bacteria_well.container.discard()
def main(p, params):
"""This protocol takes a tube of bacteria, amplifies it, and creates/stores new tubes of frozen cells
"""
#bacterial protocol
p.mammalian_cell_mode = False
amplify_and_freeze_bacteria(
p, params['bacteria_well'],
Antibiotic.from_string(params['antibiotic'])
if params['antibiotic'] != 'cell_line' else None,
Antibiotic.from_string(params['second_antibiotic'])
if params['second_antibiotic'] != 'cell_line' else None,
params['destroy_source_tube'])
if __name__ == '__main__':
run(main, "BacteriaFreezing")
from __future__ import print_function
from transcriptic_tools.utils import ml, ul
from transcriptic_tools.harness import run
from transcriptic_tools.custom_protocol import CustomProtocol as Protocol
from autoprotocol.protocol import Container
def main(p, params):
assert isinstance(p, Protocol)
#create a container
container = p.ref(params['container_name'],
cont_type=params['container_type'],
storage=params['storage_conditions'],
discard=False)
p.provision_by_name('water', container.all_wells(),
ul(params['volume_ul']))
if __name__ == '__main__':
run(main, "CreateWaterContainer")
discard=True).well(0)
#keep ul(25) to make the safe volume
p.transfer(pellet_well, trash_well, pellet_well.volume-ul(25), one_source=True, one_tip=True)
p.provision_by_name(Reagent.glycerol, pellet_well, ul(15),mix_after=True)
#remove max (this means the remaining volume is 20% glycerol)
p.transfer(pellet_well, trash_well, get_volume(pellet_well,aspiratable=True), one_source=True, one_tip=True)
if destroy_source_tube:
source_bacteria_well.container.discard()
def main(p, params):
"""This protocol takes a tube of bacteria, amplifies it, pellets the results. It can optionally induce additional BAC plasmids with IPTG
"""
#bacterial protocol
p.mammalian_cell_mode = False
pellet_bacteria(p, params['bacteria_well'],
Antibiotic.from_string(params['antibiotic']) if params['antibiotic'] != 'cell_line' else None,
params['destroy_source_tube'],
params['induce_high_copy_number']
)
if __name__ == '__main__':
run(main, "BacteriaPelleting")
primer1_well_or_reagent = get_reagent_by_transcritpic_resource_id(
resource_id, fail_if_not_found=True)
else:
primer1_well_or_reagent = params['primer_type1']['inputs'][
'custom_inventory']['primer_well']
if params['primer_type2']['value'] == 'stock':
resource_id = params['primer_type2']['inputs']['stock']['resource_id']
primer2_well_or_reagent = get_reagent_by_transcritpic_resource_id(
resource_id, fail_if_not_found=True)
else:
primer2_well_or_reagent = params['primer_type2']['inputs'][
'custom_inventory']['primer_well']
p.pcr(
template_well=params['template_well'],
primer1_well_or_reagent=primer1_well_or_reagent,
primer2_well_or_reagent=primer2_well_or_reagent,
annealing_temp_c=params['annealing_temp_c'],
greater_than_65_percent_gc_primer=params['greater_than_65_percent_gc'],
product_length=params['product_length'],
product_name=params['product_name'])
if __name__ == '__main__':
run(main, "PCR")
final_growth_well.name = miniprep_result_plate.name
p.miniprep(final_growth_well,miniprep_result_well)
p.measure_concentration(miniprep_result_well, "dna concentration", 'DNA')
if destroy_source_tube:
source_bacteria_well.container.discard()
def main(p, params):
"""This protocol takes a tube of bacteria, amplifies it, and creates/stores new tubes of frozen cells
"""
#bacterial protocol
p.mammalian_cell_mode = False
miniprep(p, params['bacteria_well'],
antibiotic=Antibiotic.from_string(params['antibiotic']) if params['antibiotic'] != 'cell_line' else None,
destroy_source_tube=params['destroy_source_tube'],
incubate_hours=params['incubate_hours'],
measure_od=params['measure_od'],
induce_high_copy_number=params['induce_high_copy_number'],
slow_growth=params['slow_growth']
)
if __name__ == '__main__':
run(main, "Miniprep")
Run a simple gel purification on one or more wells with dna
"""
assert isinstance(p, Protocol)
source_wells = []
dna_lengths = []
for dna_well in dna_wells:
source_wells.append(dna_well)
dna_lengths.append(int(dna_well.properties['dna_length']))
dest_wells = p.simple_gel_purify(source_wells, dna_lengths)
if measure_concentratio:
p.measure_concentration(dest_wells, 'dna_concentration', 'DNA')
def main(p, params):
"""This protocol takes a tube of bacteria, amplifies it, and creates/stores new tubes of frozen cells
"""
#bacterial protocol
p.mammalian_cell_mode = False
get_purify(p, params['source_dna'], params['measure_concentration'])
if __name__ == '__main__':
run(main, "GelPurify")