def build_bowtie2db(ifn_markers, tmp_dir, error_pipe=None):
# build bowtie2-index
if not os.path.isfile(ifn_markers):
error = 'ifn_markers %s does not exist!' % ifn_markers
logger.error(error)
raise Exception(error)
if not os.path.isdir(tmp_dir):
ooSubprocess.mkdir(tmp_dir)
bt2_base = ooSubprocess.splitext(ifn_markers)[0]
index_fns = glob.glob('%s/%s.*' % (tmp_dir, bt2_base))
index_path = os.path.join(tmp_dir, bt2_base)
oosp = ooSubprocess.ooSubprocess(tmp_dir)
if index_fns == []:
oosp.ex('bowtie2-build', ['--quiet', ifn_markers, index_path],
stderr=error_pipe)
else:
logger.warning('bowtie2-indexes of %s are ready, skip rebuilding!' %
(bt2_base))
return index_path
def main(args):
ooSubprocess.mkdir(args['output_dir'])
manager = multiprocessing.Manager()
if args['input_type'] == 'fastq':
index_path = build_bowtie2db(args['ifn_markers'], args['output_dir'])
args['index_path'] = index_path
args_list = []
for ifn_sample in args['ifn_samples']:
args_list.append([ifn_sample, args])
#ooSubprocess.parallelize(run_sample, args_list, args['nprocs'])
pool = multiprocessing.Pool(args['nprocs'])
results = []
for a in args_list:
r = pool.apply_async(run_sample, [a])
results.append(r)
for r in results:
try:
r.get()
except Exception as e:
print e