def copy_layout(lims, process_id):
"""Copy placement layout from previous steps."""
process = Process(lims, id=process_id)
used_placements = []
# Get parent container layout
parent_container = None
for parent_process in process.parent_processes():
if parent_process:
for container in parent_process.output_containers():
if container.type != Containertype(lims, id='2'): # skip tubes
parent_container = container
if parent_container:
parent_placements = {}
for placement in parent_container.placements:
sample = parent_container.placements[placement].samples[0].name
parent_placements[sample] = placement
# Create new container and copy layout
new_container = Container.create(lims, type=parent_container.type)
placement_list = []
for artifact in process.analytes()[0]:
sample_name = artifact.samples[0].name
if sample_name in parent_placements:
placement = parent_placements[sample_name]
if placement not in used_placements:
placement_list.append([artifact, (new_container, placement)])
used_placements.append(placement)
process.step.placements.set_placement_list(placement_list)
process.step.placements.post()
def main(lims, args):
log = []
content = None
process = Process(lims, id=args.pid)
# Copy Read and index parameter from the step "Load to Flowcell (NovaSeq 6000 v2.0)"
UDF_to_copy = [
'Read 1 Cycles', 'Read 2 Cycles', 'Index Read 1', 'Index Read 2'
]
for i in UDF_to_copy:
if process.parent_processes()[0].udf.get(i):
process.udf[i] = process.parent_processes()[0].udf[i]
process.put()
# Fetch Flowcell ID
FCID = process.parent_processes()[0].output_containers()[0].name
for outart in process.all_outputs():
if outart.type == 'ResultFile' and outart.name == 'Run Info':
try:
lims.upload_new_file(
outart,
max(glob.glob(
'/srv/mfs/NovaSeq_data/*{}/RunInfo.xml'.format(FCID)),
key=os.path.getctime))
except:
raise RuntimeError("No RunInfo.xml Found!")
elif outart.type == 'ResultFile' and outart.name == 'Run Parameters':
try:
lims.upload_new_file(
outart,
max(glob.glob(
'/srv/mfs/NovaSeq_data/*{}/RunParameters.xml'.format(
FCID)),
key=os.path.getctime))
except:
raise RuntimeError("No RunParameters.xml Found!")
def samplesheet_purify(lims, process_id, output_file):
"""Create Hamilton samplesheet for purifying 96 well plate."""
output_file.write(
'SampleID\tSample Rack barcode\tSample rack positionID\tSample Start volume\n'
)
process = Process(lims, id=process_id)
parent_process_barcode = process.parent_processes()[0].output_containers(
)[0].name
well_plate = {}
for placement, artifact in process.output_containers(
)[0].placements.iteritems():
placement = ''.join(placement.split(':'))
well_plate[placement] = artifact.samples[0].udf['Dx Fractienummer']
for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
output_file.write(
'{sample}\t{sample_rack_barcode}\t{sample_rack_position}\t{sample_start_volume}\n'
.format(sample=well_plate[well],
sample_rack_barcode=parent_process_barcode,
sample_rack_position=well,
sample_start_volume='50'))
def samplesheet_normalise(lims, process_id, output_file):
"""Create Caliper samplesheet for normalising 96 well plate."""
output_file.write(
'Monsternummer\tPlate_Id_input\tWell\tPlate_Id_output\tPipetteervolume DNA (ul)\tPipetteervolume H2O (ul)\n'
)
process = Process(lims, id=process_id)
process_samples = [artifact.name for artifact in process.analytes()[0]]
parent_processes = []
parent_process_barcode_manual = 'None'
parent_process_barcode_hamilton = 'None'
for p in process.parent_processes():
if p.type.name.startswith('Dx manueel gezuiverd placement'):
for pp in p.parent_processes():
parent_processes.append(pp)
parent_process_barcode_manual = p.output_containers()[0].name
elif p.type.name.startswith('Dx Hamilton'):
parent_processes.append(p)
parent_process_barcode_hamilton = p.output_containers()[0].name
elif p.type.name.startswith('Dx Zuiveren gDNA manueel'):
parent_processes.append(p)
if parent_process_barcode_hamilton != 'None':
parent_process_barcode = parent_process_barcode_hamilton
else:
parent_process_barcode = parent_process_barcode_manual
# Get all Qubit and Tecan Spark QC types
qc_process_types = clarity_epp.export.utils.get_process_types(
lims, ['Dx Qubit QC', 'Dx Tecan Spark 10M QC'])
# Get all unique input artifact ids
parent_processes = list(set(parent_processes))
input_artifact_ids = []
for p in parent_processes:
for analyte in p.all_outputs():
input_artifact_ids.append(analyte.id)
input_artifact_ids = list(set(input_artifact_ids))
# Get unique QC processes for input artifacts
qc_processes = list(
set(
lims.get_processes(type=qc_process_types,
inputartifactlimsid=input_artifact_ids)))
samples_measurements_qubit = {}
sample_concentration = {}
samples_measurements_tecan = {}
filled_wells = []
order = [
'A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1', 'A2', 'B2', 'C2', 'D2',
'E2', 'F2', 'G2', 'H2', 'A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3', 'H3',
'A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4', 'A5', 'B5', 'C5', 'D5',
'E5', 'F5', 'G5', 'H5', 'A6', 'B6', 'C6', 'D6', 'E6', 'F6', 'G6', 'H6',
'A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7', 'A8', 'B8', 'C8', 'D8',
'E8', 'F8', 'G8', 'H8', 'A9', 'B9', 'C9', 'D9', 'E9', 'F9', 'G9', 'H9',
'A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10', 'A11', 'B11',
'C11', 'D11', 'E11', 'F11', 'G11', 'H11', 'A12', 'B12', 'C12', 'D12',
'E12', 'F12', 'G12', 'H12'
]
order = dict(zip(order, range(len(order))))
last_filled_well = 0
monsternummer = {}
volume_DNA = {}
volume_H2O = {}
conc_measured = {}
output_ng = float(process.udf['Output genormaliseerd gDNA'])
conc = {}
output_ul = process.udf['Eindvolume (ul) genormaliseerd gDNA']
output_plate_barcode = process.output_containers()[0].name
for qc_process in qc_processes:
if 'Dx Qubit QC' in qc_process.type.name:
for artifact in qc_process.all_outputs():
sample = artifact.samples[0].name
if sample in process_samples and not any(
keyword in artifact.name
for keyword in ['Tecan', 'check', 'Label']):
if 'Dx Conc. goedgekeurde meting (ng/ul)' in artifact.udf:
measurement = artifact.udf[
'Dx Conc. goedgekeurde meting (ng/ul)']
if sample not in samples_measurements_qubit:
samples_measurements_qubit[sample] = []
samples_measurements_qubit[sample].append(measurement)
elif sample not in sample_concentration:
sample_concentration[sample] = 'geen'
elif 'Dx Tecan Spark 10M QC' in qc_process.type.name:
for artifact in qc_process.all_outputs():
sample = artifact.samples[0].name
if sample in process_samples and not any(
keyword in artifact.name
for keyword in ['Tecan', 'check', 'Label']):
if 'Dx Conc. goedgekeurde meting (ng/ul)' in artifact.udf:
measurement = artifact.udf[
'Dx Conc. goedgekeurde meting (ng/ul)']
if sample not in samples_measurements_tecan:
samples_measurements_tecan[sample] = []
samples_measurements_tecan[sample].append(measurement)
elif sample not in sample_concentration:
sample_concentration[sample] = 'geen'
for qc_process in qc_processes:
for artifact in qc_process.all_outputs():
sample = artifact.samples[0].name
if not any(keyword in artifact.name
for keyword in ['Tecan', 'check', 'Label']):
if 'Dx Tecan Spark 10M QC' in qc_process.type.name and 'Dx Conc. goedgekeurde meting (ng/ul)' in artifact.udf:
machine = 'Tecan'
elif 'Dx Qubit QC' in qc_process.type.name and 'Dx Conc. goedgekeurde meting (ng/ul)' in artifact.udf:
machine = 'Qubit'
if sample not in sample_concentration or machine == 'Qubit':
if sample in samples_measurements_tecan or sample in samples_measurements_qubit:
if machine == 'Tecan':
sample_measurements = samples_measurements_tecan[
sample]
elif machine == 'Qubit':
sample_measurements = samples_measurements_qubit[
sample]
sample_measurements_average = sum(
sample_measurements) / float(
len(sample_measurements))
sample_concentration[
sample] = sample_measurements_average
for placement, artifact in process.output_containers()[0].placements.items(
):
placement = ''.join(placement.split(':'))
filled_wells.append(placement)
if order[placement] > last_filled_well:
last_filled_well = order[placement]
for x in range(0, last_filled_well):
for well, number in order.items():
if number == x:
placement = well
monsternummer[placement] = 'Leeg'
volume_DNA[placement] = 0
volume_H2O[placement] = 0
for placement, artifact in process.output_containers()[0].placements.items(
):
sample = artifact.samples[0].name
if sample in process_samples:
placement = ''.join(placement.split(':'))
monsternummer[placement] = sample
conc_measured[placement] = sample_concentration[sample]
if conc_measured[placement] != 'geen':
if output_ng / conc_measured[placement] > 100:
conc[placement] = output_ng / 100
else:
conc[placement] = conc_measured[placement]
volume_DNA[placement] = int(round(output_ng / conc[placement]))
volume_H2O[placement] = output_ul - int(
round(output_ng / conc[placement]))
for well in clarity_epp.export.utils.sort_96_well_plate(
monsternummer.keys()):
output_file.write(
'{monsternummer}\t{plate_id_input}\t{position}\t{plate_id_output}\t{volume_DNA}\t{volume_H2O}\n'
.format(monsternummer=monsternummer[well],
plate_id_input=parent_process_barcode,
position=well,
plate_id_output=output_plate_barcode,
volume_DNA=volume_DNA[well],
volume_H2O=volume_H2O[well]))
