def main(args):
core.check_dependencies(args)
# setup logging
log, my_name = setup_logging(args)
# setup config instance
conf = ConfigParser.ConfigParser()
# preserve case of entries & read
conf.optionxform = str
conf.read(args.config)
# setup multiprocessing
pool = core.setup_multiprocessing(args)
reads = []
for start_name, end_name in conf.items('names'):
reads.append(core.SequenceData(args, conf, start_name, end_name))
# create the output directory if not exists
core.create_new_dirs(reads)
# create the set of work for each process
work = [[args, read] for read in reads]
# let us know that read cleaning has started
log.info("Trimming samples with Trimmomatic")
# start the cleaning process and output dots to indicate file progress
sys.stdout.write("Running")
sys.stdout.flush()
if pool is not None:
pool.map(core.runner, work)
else:
map(core.runner, work)
# push the output down to next line
print ""
text = " Completed {} ".format(my_name)
log.info(text.center(65, "="))
def s2():
args = TruHTFakeArgs()
conf = configparser.ConfigParser()
# preserve case of entries & read
conf.optionxform = str
conf.read(args.config)
reads = []
for start_name, end_name in conf.items("names"):
reads.append(core.SequenceData(args, conf, start_name, end_name))
return reads[1]