コード例 #1
0
ファイル: partis.py プロジェクト: stevenweaver/partis
    all_random_ints = []
    for iproc in range(args.n_procs):  # have to generate these all at once, 'cause each of the subprocesses is going to reset its seed and god knows what happens to our seed at that point
        all_random_ints.append([random.randint(0, sys.maxint) for i in range(n_per_proc)])
    for iproc in range(args.n_procs):
        proc = Process(target=make_events, args=(n_per_proc, iproc, all_random_ints[iproc]))
        proc.start()
    while len(active_children()) > 0:
        # print ' wait %s' % len(active_children()),
        sys.stdout.flush()
        time.sleep(1)
    utils.merge_csvs(args.outfname, [args.workdir + '/recombinator-' + str(iproc) + '/' + os.path.basename(args.outfname) for iproc in range(args.n_procs)], cleanup=(not args.no_clean))

if args.action == 'simulate' or args.action == 'generate-trees':
    if args.action == 'generate-trees':
        from treegenerator import TreeGenerator, Hist
        treegen = TreeGenerator(args, args.parameter_dir + '/mean-mute-freqs.csv')
        treegen.generate_trees(args.outfname)
        sys.exit(0)
    # if not args.no_clean:
    #     os.rmdir(reco.workdir)
    from recombinator import Recombinator
    run_simulation(args)
else:
    start = time.time()
    from partitiondriver import PartitionDriver
    random.seed(args.seed)
    args.queries = utils.get_arg_list(args.queries)
    args.reco_ids = utils.get_arg_list(args.reco_ids)
    args.n_max_per_region = utils.get_arg_list(args.n_max_per_region, intify=True)
    args.match_mismatch = utils.get_arg_list(args.match_mismatch, intify=True)
    args.annotation_clustering_thresholds = utils.get_arg_list(args.annotation_clustering_thresholds, floatify=True)
コード例 #2
0
    utils.merge_csvs(args.outfname, [args.workdir + '/recombinator-' + str(iproc) + '/' + os.path.basename(args.outfname) for iproc in range(args.n_procs)], cleanup=(not args.no_clean))

# ----------------------------------------------------------------------------------------
def make_events(args, n_events, iproc, random_ints):
    # NOTE all the different seeds! this sucks but is necessary
    reco = Recombinator(args, seed=args.seed+iproc, sublabel=str(iproc))  #, total_length_from_right=args.total_length_from_right)
    for ievt in range(n_events):
        # print ievt,
        # sys.stdout.flush()
        reco.combine(random_ints[ievt])

# ----------------------------------------------------------------------------------------
if args.action == 'simulate' or args.action == 'generate-trees':
    if args.action == 'generate-trees':
        from treegenerator import TreeGenerator, Hist
        treegen = TreeGenerator(args, args.parameter_dir + '/mean-mute-freqs.csv')
        treegen.generate_trees(self.args.outfname)
        sys.exit(0)
    # if not args.no_clean:
    #     os.rmdir(reco.workdir)
    from recombinator import Recombinator
    run_simulation(args)
else:
    from partitiondriver import PartitionDriver

    args.queries = utils.get_arg_list(args.queries, intify=False)
    args.reco_ids = utils.get_arg_list(args.reco_ids, intify=True)
    args.n_max_per_region = utils.get_arg_list(args.n_max_per_region)
    if len(args.n_max_per_region) != 3:
        raise Exception('ERROR n-max-per-region should be of the form \'x:y:z\', but I got' + str(args.n_max_per_region))