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))