def main():
time1 = time.time()
(options, args) = parseCommand()
dashplace = 1
for argv in sys.argv[1:]:
if argv.startswith("-"):
break
dashplace += 1
if dashplace <= 1:
runInFolder()
return
bp = BubbleProcesser(sys.argv[1:dashplace], options.poly_max,
options.output, options.draw)
circles = bp.run()
if len(circles) > 0:
print("detected bubbles:")
print(circles)
else:
print("no bubble detected")
writeCircles(circles, options.output)
time2 = time.time()
print('Time used: ' + str(time2 - time1))
def debubbleDir(folder, poly_max, output, drawImage):
files = os.listdir(folder)
fastqs = []
for f in files:
path = os.path.join(folder, f)
if os.path.isdir(path):
continue
if fastq.isFastq(path):
fastqs.append(path)
bp = BubbleProcesser(fastqs, poly_max, output, drawImage)
circles = bp.run()
if len(circles) >0 :
print("detected bubbles:")
print(circles)
else:
print("no bubble detected")
writeCircles(circles, output)
def debubbleDir(folder, poly_max, output, drawImage):
files = os.listdir(folder)
fastqs = []
for f in files:
path = os.path.join(folder, f)
if os.path.isdir(path):
continue
if fastq.isFastq(path):
fastqs.append(path)
bp = BubbleProcesser(fastqs, poly_max, output, drawImage)
circles = bp.run()
if len(circles) > 0:
print("detected bubbles:")
print(circles)
else:
print("no bubble detected")
writeCircles(circles, output)
def main():
time1 = time.time()
(options, args) = parseCommand()
dashplace = 1
for argv in sys.argv[1:]:
if argv.startswith("-"):
break
dashplace += 1
if dashplace <= 1:
runInFolder()
return
bp = BubbleProcesser(sys.argv[1:dashplace], options.poly_max, options.output, options.draw)
circles = bp.run()
if len(circles) >0 :
print("detected bubbles:")
print(circles)
else:
print("no bubble detected")
writeCircles(circles, options.output)
time2 = time.time()
print('Time used: ' + str(time2-time1))
