parser.add_argument('-N','--nsamples',default=10000,type=int ,help="Number of winows to sample.") parser.add_argument('-w','--window',default=1000, type=int ,help="Size of windows to examine.") parser.add_argument('-W','--binwindow',default=100000, type=int ,help="Size of windows to break reference contigs into.") parser.add_argument('-i','--infile',default=False ,help="Filename for serialised assembly input file.") # parser.add_argument('-o','--outfile',default=False,help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.") args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) n=0 asf.binsize = args.binwindow while n<args.nsamples: try: c,a,b=asf.random_window(wlen=args.window) if args.test: m=re.match("^(.*):(\d+)-(\d+)$",args.test) c=m.group(1) a=int(m.group(2)) b=int(m.group(3)) asf.window_stats(c,a,b,debug=args.debug,bins=args.bin) n+=1 except Exception as e: print("#",e,c,a,b) raise e if args.test: break
help="Size of windows to break reference contigs into.") parser.add_argument('-i', '--infile', default=False, help="Filename for serialised assembly input file.") # parser.add_argument('-o','--outfile',default=False,help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.") args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) n = 0 asf.binsize = args.binwindow while n < args.nsamples: try: c, a, b = asf.random_window(wlen=args.window) if args.test: m = re.match("^(.*):(\d+)-(\d+)$", args.test) c = m.group(1) a = int(m.group(2)) b = int(m.group(3)) asf.window_stats(c, a, b, debug=args.debug, bins=args.bin) n += 1 except Exception as e: print("#", e, c, a, b) raise e if args.test: break