
import argparse
import json

def main():
	
	args = getShellArguments()

	if (args.readsDir[-1] != "/"):
		args.readsDir = args.readsDir + "/"

	inputs = getSimulationInputs(args.inputJSON)

	writeSimulationSampleList(args, inputs)



def getShellArguments():
	'''
	Get shell enviroment arguments
	'''
	parser = argparse.ArgumentParser()

	parser.add_argument(
		'--inputJSON', 
		type=str, 
		help='ID of simulated cohort')
	parser.add_argument(
		'--readsDir',
		type=str,
		help='path to directory were the simulated reads files are saved')

	return parser.parse_args()


def getSimulationInputs(inputJSON):
	f = open(inputJSON,) 
	data = json.load(f) 	  
	f.close()
	return data

def writeSimulationSampleList(args, inputs):
	sampleListFileName = args.readsDir + inputs['cohort_id'] + ".samples.list"
	sampleList = open(sampleListFileName, "w")
	sampleList.write("# sample list for cohort: " + inputs['cohort_id'] + "\n")
	for i in range(inputs['n_samples']):
		sampleList.write(f"s_{i}\t{inputs['cohort_id']}.s_{i}.raw_1P.fq\t{inputs['cohort_id']}.s_{i}.raw_2P.fq\tILLUMINA\n")
	sampleList.close()


if __name__ == '__main__':
	main()
084743e94a8897efd969e94bfec2503879c3ce0f
<mask token>


def main():
    args = getShellArguments()
    if args.readsDir[-1] != '/':
        args.readsDir = args.readsDir + '/'
    inputs = getSimulationInputs(args.inputJSON)
    writeSimulationSampleList(args, inputs)


def getShellArguments():
    """
	Get shell enviroment arguments
	"""
    parser = argparse.ArgumentParser()
    parser.add_argument('--inputJSON', type=str, help='ID of simulated cohort')
    parser.add_argument('--readsDir', type=str, help=
        'path to directory were the simulated reads files are saved')
    return parser.parse_args()


<mask token>


def writeSimulationSampleList(args, inputs):
    sampleListFileName = args.readsDir + inputs['cohort_id'] + '.samples.list'
    sampleList = open(sampleListFileName, 'w')
    sampleList.write('# sample list for cohort: ' + inputs['cohort_id'] + '\n')
    for i in range(inputs['n_samples']):
        sampleList.write(
            f"""s_{i}	{inputs['cohort_id']}.s_{i}.raw_1P.fq	{inputs['cohort_id']}.s_{i}.raw_2P.fq	ILLUMINA
"""
            )
    sampleList.close()


<mask token>

<mask token>


def main():
    args = getShellArguments()
    if args.readsDir[-1] != '/':
        args.readsDir = args.readsDir + '/'
    inputs = getSimulationInputs(args.inputJSON)
    writeSimulationSampleList(args, inputs)


def getShellArguments():
    """
	Get shell enviroment arguments
	"""
    parser = argparse.ArgumentParser()
    parser.add_argument('--inputJSON', type=str, help='ID of simulated cohort')
    parser.add_argument('--readsDir', type=str, help=
        'path to directory were the simulated reads files are saved')
    return parser.parse_args()


def getSimulationInputs(inputJSON):
    f = open(inputJSON)
    data = json.load(f)
    f.close()
    return data


def writeSimulationSampleList(args, inputs):
    sampleListFileName = args.readsDir + inputs['cohort_id'] + '.samples.list'
    sampleList = open(sampleListFileName, 'w')
    sampleList.write('# sample list for cohort: ' + inputs['cohort_id'] + '\n')
    for i in range(inputs['n_samples']):
        sampleList.write(
            f"""s_{i}	{inputs['cohort_id']}.s_{i}.raw_1P.fq	{inputs['cohort_id']}.s_{i}.raw_2P.fq	ILLUMINA
"""
            )
    sampleList.close()


<mask token>

<mask token>


def main():
    args = getShellArguments()
    if args.readsDir[-1] != '/':
        args.readsDir = args.readsDir + '/'
    inputs = getSimulationInputs(args.inputJSON)
    writeSimulationSampleList(args, inputs)


def getShellArguments():
    """
	Get shell enviroment arguments
	"""
    parser = argparse.ArgumentParser()
    parser.add_argument('--inputJSON', type=str, help='ID of simulated cohort')
    parser.add_argument('--readsDir', type=str, help=
        'path to directory were the simulated reads files are saved')
    return parser.parse_args()


def getSimulationInputs(inputJSON):
    f = open(inputJSON)
    data = json.load(f)
    f.close()
    return data


def writeSimulationSampleList(args, inputs):
    sampleListFileName = args.readsDir + inputs['cohort_id'] + '.samples.list'
    sampleList = open(sampleListFileName, 'w')
    sampleList.write('# sample list for cohort: ' + inputs['cohort_id'] + '\n')
    for i in range(inputs['n_samples']):
        sampleList.write(
            f"""s_{i}	{inputs['cohort_id']}.s_{i}.raw_1P.fq	{inputs['cohort_id']}.s_{i}.raw_2P.fq	ILLUMINA
"""
            )
    sampleList.close()


if __name__ == '__main__':
    main()

import argparse
import json


def main():
    args = getShellArguments()
    if args.readsDir[-1] != '/':
        args.readsDir = args.readsDir + '/'
    inputs = getSimulationInputs(args.inputJSON)
    writeSimulationSampleList(args, inputs)


def getShellArguments():
    """
	Get shell enviroment arguments
	"""
    parser = argparse.ArgumentParser()
    parser.add_argument('--inputJSON', type=str, help='ID of simulated cohort')
    parser.add_argument('--readsDir', type=str, help=
        'path to directory were the simulated reads files are saved')
    return parser.parse_args()


def getSimulationInputs(inputJSON):
    f = open(inputJSON)
    data = json.load(f)
    f.close()
    return data


def writeSimulationSampleList(args, inputs):
    sampleListFileName = args.readsDir + inputs['cohort_id'] + '.samples.list'
    sampleList = open(sampleListFileName, 'w')
    sampleList.write('# sample list for cohort: ' + inputs['cohort_id'] + '\n')
    for i in range(inputs['n_samples']):
        sampleList.write(
            f"""s_{i}	{inputs['cohort_id']}.s_{i}.raw_1P.fq	{inputs['cohort_id']}.s_{i}.raw_2P.fq	ILLUMINA
"""
            )
    sampleList.close()


if __name__ == '__main__':
    main()


import argparse
import json

def main():
	
	args = getShellArguments()

	if (args.readsDir[-1] != "/"):
		args.readsDir = args.readsDir + "/"

	inputs = getSimulationInputs(args.inputJSON)

	writeSimulationSampleList(args, inputs)



def getShellArguments():
	'''
	Get shell enviroment arguments
	'''
	parser = argparse.ArgumentParser()

	parser.add_argument(
		'--inputJSON', 
		type=str, 
		help='ID of simulated cohort')
	parser.add_argument(
		'--readsDir',
		type=str,
		help='path to directory were the simulated reads files are saved')

	return parser.parse_args()


def getSimulationInputs(inputJSON):
	f = open(inputJSON,) 
	data = json.load(f) 	  
	f.close()
	return data

def writeSimulationSampleList(args, inputs):
	sampleListFileName = args.readsDir + inputs['cohort_id'] + ".samples.list"
	sampleList = open(sampleListFileName, "w")
	sampleList.write("# sample list for cohort: " + inputs['cohort_id'] + "\n")
	for i in range(inputs['n_samples']):
		sampleList.write(f"s_{i}\t{inputs['cohort_id']}.s_{i}.raw_1P.fq\t{inputs['cohort_id']}.s_{i}.raw_2P.fq\tILLUMINA\n")
	sampleList.close()


if __name__ == '__main__':
	main()