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)
if len(args.n_max_per_region) != 3:
raise Exception('n-max-per-region should be of the form \'x:y:z\', but I got ' + str(args.n_max_per_region))
if len(args.match_mismatch) != 2:
raise Exception('match-mismatch should be of the form \'match:mismatch\', but I got ' + str(args.n_max_per_region))
parter = PartitionDriver(args)
if args.action == 'build-hmms': # just build hmms without doing anything else -- you wouldn't normally do this
parter.write_hmms(args.parameter_dir)
elif args.action == 'cache-parameters':
parter.cache_parameters()
elif 'run-' in args.action:
parter.run_algorithm(args.action.replace('run-', ''))
elif args.action == 'partition':
parter.partition()
else:
raise Exception('ERROR bad action ' + args.action)
parter.clean()
print ' total time: %.3f' % (time.time()-start)
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))
utils.prep_dir(args.workdir)
parter = PartitionDriver(args)
if args.action == 'build-hmms': # just build hmms without doing anything else -- you wouldn't normally do this
parter.write_hmms(args.parameter_dir, None)
sys.exit()
elif args.action == 'cache-parameters':
parter.cache_parameters()
elif 'run-' in args.action:
parter.run_algorithm(args.action.replace('run-', ''))
elif args.action == 'partition':
parter.partition()
else:
raise Exception('ERROR bad action ' + args.action)
