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)
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))