nodes = {} range_cutoff = args.range_cutoff t1 = args.end_threshold t2 = args.support_cutoff # recombinings2.max_n_breaks=args.max_n_breaks fmodel = open(args.set_insert_size_dist_fit_params) contents = fmodel.read() try: fit_params = eval(contents) except: "couldn't deal with option", args.param fmodel.close ces.set_exp_insert_size_dist_fit_params(fit_params) cache_cutoff = 150000 log_score_cache = {} bamfiles = args.bamfiles.split(",") contigs = [] chunkf = open(args.chunk, "rt") while True: l = chunkf.readline() if not l: break contigs.append(l.strip()) chunkf.close() oname = {}
args = parser.parse_args() if args.top: import psutil hra = HiriseAssembly() hra.load_assembly(args.infile) hra.merge_masked_regions(debug=args.debug) print(len(hra.layout_lines)) if len(hra.layout_lines) == 0: print("#make trivial layout") hra.make_trivial_layout_lines(debug=args.debug) ces.set_exp_insert_size_dist_fit_params(hra.model_params) model = ces.model nbams = len(hra.bams) inq = JoinableQueue(maxsize=0) readers = [] for i in range(nbams): reader = Process(target=read_pairs_from_bam, args=(inq, i, hra.bams[i], hra, args.mapq, args.slice), daemon=False) reader.start() readers.append(reader) q = JoinableQueue(maxsize=0) histogram_queue = JoinableQueue(maxsize=0)
def set_fit_params(fit_params): ces.set_exp_insert_size_dist_fit_params(fit_params)
args = parser.parse_args() if args.top: import psutil hra = HiriseAssembly() hra.load_assembly(args.infile) hra.merge_masked_regions(debug=args.debug) print(len(hra.layout_lines)) if len(hra.layout_lines)==0: print("#make trivial layout") hra.make_trivial_layout_lines(debug=args.debug) ces.set_exp_insert_size_dist_fit_params(hra.model_params) model=ces.model nbams = len(hra.bams) inq = JoinableQueue(maxsize=0) readers=[] for i in range(nbams): reader = Process(target=read_pairs_from_bam, args=(inq,i,hra.bams[i],hra,args.mapq,args.slice),daemon=False) reader.start() readers.append(reader) q = JoinableQueue(maxsize=0) histogram_queue = JoinableQueue(maxsize=0) final_histogram_queue = JoinableQueue(maxsize=0) outfiles = [ open("{}.part.{}".format(args.outfile,i),"wt") for i in range(args.nthreads) ]