''' Prepare '''
print os.getcwd()
#tmpdir='./tmp_'+datetime.now().strftime('%Y%m%d%H%M%S')
#os.mkdir(tmpdir)
t_pool = ThreadPool(opts.thread)
''' Read Sample Files (Concurrent by sample)'''
for m, sample_arg in enumerate(args):
replist = sample_arg.split(',')
for n, replicate_file in enumerate(replist):
if not os.path.exists(replicate_file):
sys.stderr.write('%d th replicate file of %d th sample (%s) doesn\'t exist' % (n+1,m+1,replicate_file))
sys.exit(1)
sample_list.append(SampleData(replist))
for m, sample_data in enumerate(sample_list):
t_pool.queueTask(preprocess_samples,sample_data,None)
t_pool.joinAll()
if DEBUG:
print "print chromosome order"
for chrom_name in sample_data.chrom_order:
print chrom_name
''' debug purpose '''
if DEBUG:
for sample_data in sample_list:
sample_data.output_debug_info()
def sample_data():
"""Returns a SampleData() object"""
from sampledata import SampleData
return SampleData()