def main(conf):
cfg = load_mirquant_config_file(conf)
outPath = create_output_folder(cfg['paths']['output'])
samples = sample_input_location(cfg['paths']['project'], cfg['paths']['output'])
mapping_stats(outPath, samples)
length_distribution(outPath, samples)
RPMMandRPMMM(cfg['parameters']['species'], outPath, samples)
def main(args):
cfg = load_mirquant_config_file(args.conf)
scfg = load_sys_config_file(args.conf)
job = build_job(scfg['job'])
sample_res = return_sample_results_directories(cfg['paths']['project'])
temp_fi = []
for sample in sample_res:
temp_fi = combine_result_files(sample, cfg, job, temp_fi, args.conf)
wait_for_collect_res(temp_fi, sample_res, job)
def main(args):
check_config_path(args.conf)
cfg = load_mirquant_config_file(args.conf)
scfg = load_sys_config_file(args.conf)
job = build_job(scfg['job'])
fastqs = get_fastqs(cfg['paths']['project'])
for sample in fastqs:
print 'Running for sample: {}'.format(sample)
os.system('{} python ./bin/chainSubmission.py {} {}'.format(job, args.conf, sample))
def main(args):
cfg = load_mirquant_config_file(args.conf)
scfg = load_sys_config_file(args.conf)
job = build_job(scfg['job'])
sample_res = return_sample_results_directories(cfg['paths']['project'])
temp_fi = []
for sample in sample_res:
print '\nRunning runC on sample {}'.format(sample)
temp_fi = combine_result_files(sample, cfg, job, temp_fi, args.conf)
wait_for_collect_res(temp_fi, sample_res, job)
def main(arg):
cfg = load_mirquant_config_file(arg.conf)
outPath = create_output_folder(cfg['paths']['output'])
samples = sample_input_location(cfg['paths']['project'], cfg['paths']['output'])
mapping_stats(cfg['paths']['project'], outPath, samples)
length_distribution(outPath, samples)
RPMMandRPMMM(cfg['parameters']['species'], cfg['paths']['project'], outPath, samples)
calculate_statistics(cfg['paths']['project'], outPath)
DESeq(cfg['paths']['project'], outPath, arg.DESeq)
assemble_xls.main(outPath)