def main(cmdl):
""" Run the script. """
from pararead import logger_via_cli
opts = _parse_cmdl(cmdl)
logger = logger_via_cli(opts)
logger.debug("Creating counter")
counter = ReadCounter(opts.readsfile,
cores=opts.cores,
outfile=opts.outfile,
action="CountReads")
logger.debug("Registering files")
counter.register_files()
logger.info("Counting reads: {}".format(opts.readsfile))
good_chromosomes = counter.run()
logger.info("Collecting read counts: {}".format(opts.outfile))
counter.combine(good_chromosomes, chrom_sep="\n")
'--outfile',
dest='outfile',
help="Output file name.")
parser.add_argument('-c',
'--cores',
dest='cores',
default=20,
type=int,
help="Number of processors to use. Default=20")
parser = add_logging_options(parser)
return parser.parse_args(cmdl)
# parallel processed computation of matrix for each chromosome
if __name__ == "__main__":
args = parse_args(sys.argv[1:])
_LOGGER = logger_via_cli(args)
qc = bamQC(reads_filename=args.infile,
out_filename=args.outfile,
n_proc=args.cores,
verbosity=args.verbosity)
qc.register_files()
good_chromosomes = qc.run()
_LOGGER.info("Reduce step (merge files)...")
qc.combine(good_chromosomes)