def _outsource_tasks(self, task_q):
with open(self.config, 'r') as fCONFIG:
blastskip = -1
cutadaptskip = -1
decontamskip = -1
for line in fCONFIG:
if not line.startswith('#') or not line.strip(): # skip comments
if line.startswith('['):
lib = line.strip().lstrip('[').rstrip(']')
elif line.startswith("dir"):
dir = line.split('=')[1].strip()
elif line.startswith('fastq'):
fq1 = os.path.join(dir, line.split('=')[1].strip().split(',')[0])
fq2 = os.path.join(dir, line.split('=')[1].strip().split(',')[1])
check_if_files_exist("Preqc", fq1, fq2)
elif line.startswith('decontamskip'):
decontamskip = int(line.split('=')[1].strip())
elif line.startswith('blastskip'):
blastskip = int(line.split('=')[1].strip())
elif line.startswith('cutadaptskip'):
cutadaptskip = int(line.split('=')[1].strip())
elif line.startswith('adapter'):
a1 = line.split('=')[1].strip().split(',')[0]
a2 = line.split('=')[1].strip().split(',')[1]
if blastskip == -1:
blastskip = 0
if cutadaptskip == -1:
cutadaptskip = 0
if decontamskip == -1:
decontamskip = 0
task_q.put((lib, fq1, fq2, blastskip, decontamskip, cutadaptskip, a1, a2))
blastskip = -1
cutadaptskip = -1
decontamskip = -1
def __init__(self, args):
self.target = os.path.realpath(args.target)
make_dir_if_necessary(self.target)
self.nproc = args.nproc
self.nthread = args.nthread
self.keep = args.keep
self.db = args.db
self.min_eval = args.min_eval
self.config = args.config
if self.db is not None:
check_if_files_exist("Preqc", self.config, self.db)
else:
check_if_files_exist("Preqc", self.config)
self.min_overlap = args.min_overlap
self.min_readlen = args.min_readlen
