def main(argv):
options = launch_options.Options(argv, spades_home, truspades_home, spades_version)
support.ensure_dir_existence(options.output_dir)
if options.test and not options.continue_launch:
support.recreate_dir(options.output_dir)
log = create_log(options)
dataset_file = os.path.join(options.output_dir, "dataset.info")
if options.continue_launch:
dataset = barcode_extraction.ReadDataset(dataset_file, log)
elif options.input_dirs is not None:
dataset = generate_dataset(options.input_dirs, log)
if dataset is None:
log.info("Error: could not parse dataset from input directories\n")
sys.exit(1)
barcode_extraction.print_dataset(dataset, dataset_file, log)
log.info("Dataset generated. See result in " + dataset_file)
else:
dataset = barcode_extraction.ReadDataset(options.dataset_file, log)
barcode_extraction.print_dataset(dataset, dataset_file, log)
log_dir = os.path.join(options.output_dir, "logs")
support.ensure_dir_existence(log_dir)
# if options.print_commands:
# verify_exists(options.output_dir)
# print_commands(commands, options)
if options.mode == "run_truspades":
RunTruSPAdes(dataset, log_dir, options, log)
elif options.mode == "construct_subreferences":
reference_construction.ConstructSubreferences(dataset, options.reference, options.output_dir, options.index, options.threads, log = None)
log.info("TruSPAdes launch successfully finished")
if options.test:
CheckTestSuccess(options, log)
def ConstructSubreferences(dataset, options):
reference_construction.ConstructSubreferences(dataset,
options.reference,
options.output_dir,
options.index,
options.threads,
log=None)