def main(args, lims, epp_logger):
p = Process(lims, id=args.pid)
lines = []
cs = []
if args.container_id:
cs = p.output_containers()
for c in cs:
logging.info('Constructing barcode for container {0}.'.format(
c.id))
lines += makeContainerBarcode(c.id, copies=1)
if args.container_name:
cs = p.output_containers()
for c in cs:
logging.info('Constructing name label for container {0}.'.format(
c.id))
lines += makeContainerNameBarcode(c.name, copies=1)
if args.operator_and_date:
op = p.technician.name
date = str(datetime.date.today())
if cs: # list of containers
copies = len(cs)
else:
copies = args.copies
lines += makeOperatorAndDateBarcode(op, date, copies=copies)
if args.process_name:
pn = p.type.name
if cs: # list of containers
copies = len(cs)
else:
copies = args.copies
lines += makeProcessNameBarcode(pn, copies=copies)
if not (args.container_id or args.container_name or args.operator_and_date
or args.process_name):
logging.info('No recognized label type given, exiting.')
sys.exit(-1)
if not args.use_printer:
logging.info('Writing to stdout.')
epp_logger.saved_stdout.write('\n'.join(lines) + '\n')
elif lines: # Avoid printing empty files
lp_args = ["lp"]
if args.hostname:
#remove that when all the calls to this script have been updated
if args.hostname == 'homer.scilifelab.se:631':
args.hostname = 'homer2.scilifelab.se:631'
lp_args += ["-h", args.hostname]
if args.destination:
lp_args += ["-d", args.destination]
lp_args.append("-") # lp accepts stdin if '-' is given as filename
logging.info('Ready to call lp for printing.')
sp = subprocess.Popen(lp_args,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
sp.stdin.write(str('\n'.join(lines)))
logging.info('lp command is called for printing.')
stdout, stderr = sp.communicate() # Will wait for sp to finish
logging.info('lp stdout: {0}'.format(stdout))
logging.info('lp stderr: {0}'.format(stderr))
logging.info('lp command finished')
sp.stdin.close()
def main(args,lims,epp_logger):
p = Process(lims,id=args.pid)
lines = []
cs = []
if args.container_id:
cs = p.output_containers()
for c in cs:
logging.info('Constructing barcode for container {0}.'.format(c.id))
lines += makeContainerBarcode(c.id, copies=1)
if args.container_name:
cs = p.output_containers()
for c in cs:
logging.info('Constructing name label for container {0}.'.format(c.id))
lines += makeContainerNameBarcode(c.name,copies=1)
if args.operator_and_date:
op = p.technician.name
date = str(datetime.date.today())
if cs: # list of containers
copies = len(cs)
else:
copies = args.copies
lines += makeOperatorAndDateBarcode(op,date,copies=copies)
if args.process_name:
pn = p.type.name
if cs: # list of containers
copies = len(cs)
else:
copies = args.copies
lines += makeProcessNameBarcode(pn,copies=copies)
if not (args.container_id or args.container_name or
args.operator_and_date or args.process_name):
logging.info('No recognized label type given, exiting.')
sys.exit(-1)
if not args.use_printer:
logging.info('Writing to stdout.')
epp_logger.saved_stdout.write('\n'.join(lines)+'\n')
elif lines: # Avoid printing empty files
lp_args = ["lp"]
if args.hostname:
#remove that when all the calls to this script have been updated
if args.hostname == 'homer.scilifelab.se:631':
args.hostname='homer2.scilifelab.se:631'
lp_args += ["-h",args.hostname]
if args.destination:
lp_args += ["-d",args.destination]
lp_args.append("-") # lp accepts stdin if '-' is given as filename
logging.info('Ready to call lp for printing.')
sp = subprocess.Popen(lp_args,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
sp.stdin.write(str('\n'.join(lines)))
logging.info('lp command is called for printing.')
stdout,stderr = sp.communicate() # Will wait for sp to finish
logging.info('lp stdout: {0}'.format(stdout))
logging.info('lp stderr: {0}'.format(stderr))
logging.info('lp command finished')
sp.stdin.close()
def samplesheet(lims, process_id, output_file):
"""Create Tapestation samplesheet."""
process = Process(lims, id=process_id)
well_plate = {}
for placement, artifact in process.output_containers(
)[0].placements.iteritems():
placement = ''.join(placement.split(':'))
well_plate[placement] = artifact.name.split('_')[0]
for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
output_file.write('{sample}\n'.format(sample=well_plate[well]))
def container_sample(lims, process_id, output_file, description=''):
"""Generate container & artifact name label file."""
process = Process(lims, id=process_id)
for container in process.output_containers():
for artifact in container.placements.values():
if description:
output_file.write(
'{description}\t{sample}\t{container}\r\n'.format(
description=description,
container=container.name,
sample=artifact.name))
else:
output_file.write('{sample}\t{container}\r\n'.format(
container=container.name, sample=artifact.name))
def samplesheet_filling_out(lims, process_id, output_file):
"""Create Hamilton samplesheet for filling out 96 well plate."""
output_file.write('SourceTubeID\tPositionID\n')
process = Process(lims, id=process_id)
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('{source_tube}\t{well}\n'.format(
source_tube=well_plate[well], well=well))
def samplesheet(lims, process_id, output_file):
"""Create Magnis samplesheet."""
process = Process(lims, id=process_id)
well_strip = {}
for placement, artifact in process.output_containers()[0].placements.items():
placement = ''.join(placement.split(':'))
well_strip[placement] = artifact.name
# Write Header
output_file.write('sample_id\n')
# Write samples
for well in clarity_epp.export.utils.sort_96_well_plate(well_strip.keys()):
output_file.write('{sample}{instrument_name}\n'.format(
sample=well_strip[well],
instrument_name=process.udf['Instrument naam'].capitalize()
))
def container(lims, process_id, output_file, description=''):
"""Generate container label file."""
process = Process(lims, id=process_id)
for index, container in enumerate(
sorted(process.output_containers(),
key=lambda container: container.id,
reverse=True)):
if description:
if ',' in description:
output_file.write('{description}\t{container}\r\n'.format(
description=description.split(',')[index],
container=container.name))
else:
output_file.write('{description}\t{container}\r\n'.format(
description=description, container=container.name))
else:
output_file.write(
'{container}\r\n'.format(container=container.name))
def samplesheet(lims, process_id, output_file):
"""Create Tecan samplesheet."""
output_file.write('Position\tSample\n')
process = Process(lims, id=process_id)
well_plate = {}
for placement, artifact in process.output_containers()[0].placements.items(
):
placement = ''.join(placement.split(':'))
if len(
artifact.samples
) == 1: # Remove 'meet_id' from artifact name if artifact is not a pool
well_plate[placement] = artifact.name.split('_')[0]
else:
well_plate[placement] = artifact.name
for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
output_file.write('{well}\t{sample}\n'.format(well=well,
sample=well_plate[well]))
def samplesheet(lims, process_id, output_file):
"""Create Bioanalyzer samplesheet."""
process = Process(lims, id=process_id)
# Default plate layout
plate = {
'A1': {'name': 'sample 1', 'comment': ''}, 'A2': {'name': 'sample 2', 'comment': ''}, 'A3': {'name': 'sample 3', 'comment': ''},
'B1': {'name': 'sample 4', 'comment': ''}, 'B2': {'name': 'sample 5', 'comment': ''}, 'B3': {'name': 'sample 6', 'comment': ''},
'C1': {'name': 'sample 7', 'comment': ''}, 'C2': {'name': 'sample 8', 'comment': ''}, 'C3': {'name': 'sample 9', 'comment': ''},
'D1': {'name': 'sample 10', 'comment': ''}, 'D2': {'name': 'sample 11', 'comment': ''}
}
# Get sample placement
for placement, artifact in process.output_containers()[0].placements.iteritems():
placement = ''.join(placement.split(':'))
plate[placement]['name'] = artifact.name
plate[placement]['comment'] = ''
# Create samplesheet
output_file.write('"Sample Name","Sample Comment","Rest. Digest","Status","Observation","Result Label","Result Color"\n')
for well in sorted(plate.keys()):
output_file.write('{sample},{sample_comment},FALSE,1,,,\n'.format(
sample=plate[well]['name'],
sample_comment=plate[well]['comment']
))
output_file.write('Ladder,,FALSE,1,,,\n\n')
output_file.write('"Chip Lot #","Reagent Kit Lot #"\n')
output_file.write('{chip_lot},{reagent_lot}\n\n'.format(
chip_lot=process.udf['lot # chip'],
reagent_lot=process.udf['lot # Reagentia kit']
))
output_file.write('"QC1 Min [%]","QC1 Max [%]","QC2 Min [%]","QC2 Max [%]"\n')
output_file.write(',,,\n\n')
output_file.write('"Chip Comment"\n\n\n')
output_file.write('"Study Name","Experimenter","Laboratory","Company","Department"\n')
output_file.write(',,,,\n\n')
output_file.write('"Study Comment"\n\n')
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_purify(lims, process_id, output_file):
"""Create manual pipetting samplesheet for purifying samples."""
output_file.write(
'Fractienummer\tConcentration(ng/ul)\taantal ng te isoleren\tul gDNA\tul Water\n'
)
process = Process(lims, id=process_id)
for container in process.output_containers():
artifact = container.placements['1:1'] # asume tubes
input_artifact = artifact.input_artifact_list()[
0] # asume one input artifact
sample = artifact.samples[0] # asume one sample per tube
if 'Dx Fractienummer' in sample.udf:
fractienummer = sample.udf['Dx Fractienummer']
else: # giab
fractienummer = sample.name
if 'Dx Concentratie fluorescentie (ng/ul)' in input_artifact.udf:
concentration = float(
input_artifact.udf['Dx Concentratie fluorescentie (ng/ul)'])
elif 'Dx Concentratie OD (ng/ul)' in input_artifact.udf:
concentration = float(
input_artifact.udf['Dx Concentratie OD (ng/ul)'])
elif 'Dx Concentratie (ng/ul)' in sample.udf:
concentration = float(sample.udf['Dx Concentratie (ng/ul)'])
input_gdna_ng = float(artifact.udf['Dx input hoeveelheid (ng)'])
ul_gdna = input_gdna_ng / concentration
ul_water = 200 - ul_gdna
output_file.write(
'{fractienummer}\t{concentration}\t{input_gdna_ng}\t{ul_gdna:.1f}\t{ul_water:.1f}\n'
.format(fractienummer=fractienummer,
concentration=concentration,
input_gdna_ng=input_gdna_ng,
ul_gdna=ul_gdna,
ul_water=ul_water))
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]))
