def test_sing_est(self):
args = [
'test_est_left_msh.txt', 'test_est_right_msh.txt', '--n', '50',
'--n0', '10000', '--mut', '1e-8', '--rec', '1e-8', '--round', '3',
'--outfn', 'test_est.txt', '--seed', '1'
]
run_estimator(args)
self.assertTrue(filecmp.cmp('test_est.txt', 'test_sing_est.txt'))
def main(argv):
parser = createParser()
if argv[-1] == '':
argv = argv[0:-1]
args = parser.parse_args(argv)
#print (args.k_list)
#exit()
## k_edges_group
if not (args.alledges or args.k1 or args.k_all or args.k_range
or args.k_list):
parser.error(
'one of [--alledges, --k1, --k-range, --k-all, --k-list] must be invoked'
)
#if not (args.alledges or args.k_all or args.k_range):
# args.k1 = True
## rec_group options
if not (args.rec_rate or args.mapname):
parser.error('one of [--rec, --map] must be invoked')
if args.msh_only and not args.outmsh:
parser.error("--outmsh must be used with --msh-only")
if args.k_range is not None and args.k_range[0] < 2:
parser.error("--k-range requires a range start 2 or greater")
if args.k_range is not None and args.k_range[0] > args.k_range[1]:
parser.error("Start of --k-range must be not be greater than end")
est_args = makemshfiles(args)
if not args.msh_only:
if args.k1:
tempstr = " tc values for singletons only "
elif args.k_all:
tempstr = " tc values for all SNPs"
elif args.k_range:
tempstr = "tc values in SNPs with counts in range {}-{} ".format(
args.k_range[0], args.k_range[1])
else:
#assert args.alledges
tempstr = "t0 values for all edges at positions"
if args.posname:
tempstr += " given in file {}".format(args.posname)
else:
tempstr += " adjacent to SNPs"
sys.stderr.write("Generating estimates (%s): %s\n" %
(tempstr, str(est_args)))
estat = run_estimator(est_args)
if not args.keep_msh_files:
if os.path.exists(est_args[0]):
os.remove(est_args[0])
if os.path.exists(est_args[1]):
os.remove(est_args[1])