def main():
start = datetime.now()
global logger
fn = os.path.join(os.getcwd(), "cLoops.log")
logger = getLogger(fn)
op = mainHelp()
report = "Command line: cLoops -f {} -o {} -m {} -eps {} -minPts {} -p {} -w {} -j {} -s {} -c {} -hic {} -cut {} -plot {} -max_cut {}".format(
op.fnIn, op.fnOut, op.mode, op.eps, op.minPts, op.cpu, op.washU,
op.juice, op.tmp, op.chroms, op.hic, op.cut, op.plot, op.max_cut)
logger.info(report)
if op.mode == 0:
#parse eps
if "," in str(op.eps):
eps = map(int, op.eps.split(","))
eps.sort(reverse=False)
else:
eps = int(op.eps)
if eps != 0:
eps = [eps]
#parse minPts
if "," in str(op.minPts):
minPts = map(int, op.minPts.split(","))
minPts.sort(reverse=True)
else:
minPts = int(op.minPts)
if minPts != 0:
minPts = [minPts]
else:
logger.error("minPts not assigned!")
return
hic = op.hic
if op.mode == 1:
eps = [500, 1000, 2000]
minPts = [5]
hic = 0
if op.mode == 2:
eps = [1000, 2000, 5000]
minPts = [5]
hic = 0
if op.mode == 3:
eps = [5000, 7500, 10000]
minPts = [50, 40, 30, 20]
hic = 1
if op.mode == 4:
eps = [2500, 5000, 7500, 10000]
minPts = [30, 20]
hic = 1
report = "mode:%s\t eps:%s\t minPts:%s\t hic:%s\t" % (op.mode, eps, minPts,
hic)
logger.info(report)
pipe(op.fnIn.split(","), op.fnOut, eps, minPts, op.chroms, op.cpu, op.tmp,
hic, op.washU, op.juice, op.cut, op.plot, op.max_cut)
usedtime = datetime.now() - start
r = "cLoops finished. Used CPU time: %s Bye!\n\n\n" % usedtime
logger.info(r)
def main():
global logger
fn = os.path.join(os.getcwd(), "quantifyLoops.log")
logger = getLogger(fn)
op = help()
if op.chroms == "":
chroms = []
else:
chroms = set(op.chroms.split(","))
cfa, dfa = op.f, op.d
ra = preDs(cfa, dfa, chroms)
keys = ra.keys()
for key in ra.keys():
if key not in keys:
del ra[key]
logger.info("No match of %s in %s or %s" % (key, cfa, dfa))
quantifyLoops(ra, op.output, op.dis, op.cpu)
def main():
start = datetime.now()
global logger
fn = os.path.join(os.getcwd(), "cLoops.log")
logger = getLogger(fn)
op = mainHelp()
report = "Command line: cLoops -f {} -o {} -eps {} -minPts {} -p {} -w {} -j {} -s {} -c {} -hic {} -cut {}".format(
op.fnIn, op.fnOut, op.eps, op.minPts, op.cpu, op.washU, op.juice,
op.tmp, op.chroms, op.hic, op.cut)
logger.info(report)
if "," in str(op.eps):
eps = map(int, op.eps.split(","))
else:
eps = int(op.eps)
if eps != 0:
eps = [eps]
pipe(op.fnIn.split(","), op.fnOut, eps, op.minPts, op.chroms, op.cpu,
op.tmp, op.hic, op.washU, op.juice, op.cut)
usedtime = datetime.now() - start
r = "cLoops finished. Used CPU time: %s Bye!" % usedtime
logger.info(r)
l, a, n, m, = 0, 0, 0, 0
for d in ds:
l += d[0]
a += d[1]
n += d[2]
m += d[3]
r = m / 1.0 / n
report = "%s\t%s,loops:%s, anchors:%s,raw PETs: %s, PETs in anchors:%s, ratio:%s" % (
f, dir, l, a, n, m, r)
logger.info(report)
if __name__ == "__main__":
start = datetime.now()
fn = os.path.join(os.getcwd(), "%s.log" % NAME)
logger = getLogger(fn)
op = jd2cleanWashuPETsHelp()
if op.chroms == "":
chroms = []
else:
chroms = set(op.chroms.split(","))
if not os.path.exists(op.output):
os.mkdir(op.output)
jd2cleanWashuPETs(op.f,
op.d,
op.significant,
op.output,
chroms=chroms,
cpu=op.cpu)
usedtime = datetime.now() - start
r = "%s finished. Bye! Used time:%s" % (NAME, usedtime)