def main(opt):
logging.getLogger().setLevel(logging.DEBUG if opt.v else logging.INFO)
base_dict = dict(lazy_wl=False,
rank_fail=True,
use_maxrep=opt.use_maxrep,
load_maxrep=opt.load_maxrep,
load_cst=opt.load_cst,
space_usage=True,
time_usage=True,
answer=False)
for i, pref in enumerate(opt.prefixes):
ispec = MsInput.basedir_form(opt.base_dir, pref)
command = MsInterface.command_from_dict(
dict(s_path=ispec.s_path, t_path=ispec.t_path, **base_dict))
for j in range(opt.repeat):
with open(opt.output, 'a') as fd:
res = get_output(command)
if i + j == 0:
fd.write(res[0] + ",label,b_path\n")
for line in res[1:]:
fd.write(
line.replace(" ", "") + ("," + opt.label) +
("," + pref) + "\n")
def main(opt):
logging.getLogger().setLevel(logging.DEBUG if opt.v else logging.INFO)
base_dict = dict(lazy_wl=opt.lazy_wl,
sada=opt.sada,
load_cst=opt.load_cst,
space_usage=True,
time_usage=True,
answer=False,
runs_progress=opt.runs_progress,
ms_progress=opt.ms_progress)
for i, pref in enumerate(opt.prefixes):
bpath = os.path.join(opt.base_dir, pref)
command = MsInterface.command_from_dict(
dict(s_path=bpath + ".s", t_path=bpath + ".t", **base_dict))
for j in range(opt.repeat):
with open(opt.output, 'a') as fd:
res = get_output(command)
if i + j == 0:
fd.write(res[0] + ",label,b_path\n")
for line in res[1:]:
fd.write(
line.replace(" ", "") + ("," + opt.label) +
("," + os.path.basename(bpath)) + "\n")
def fast(opt, ms_input):
params = dict(lazy_wl=opt.lazy_wl,
rank_fail=opt.rank_fail,
lca_parents=opt.lca_parents,
use_maxrep=opt.use_maxrep,
nthreads=opt.nthreads,
answer=True,
s_path=ms_input.s_path,
t_path=ms_input.t_path)
return MsInterface.command_from_dict(params)
def main(opt):
logging.getLogger().setLevel(logging.DEBUG if opt.v else logging.INFO)
if opt.output != '/dev/stdout' and os.path.exists(opt.output):
LG.error("output file (%s) exsts. Exiting ...", opt.output)
return 1
command = MsInterface.command_from_dict(vars(opt))
pref = os.path.basename(opt.s_path).replace(".s", "")
header_suff = ",".join(['label', opt.repeat_colname, 'b_path'])
for j in range(opt.repeat):
with open(opt.output, 'a') as fd:
res = get_output(command)
if j == 0:
fd.write(res[0] + "," + header_suff + "\n")
for line in res[1:]:
fd.write(line.replace(" ", "") +
("," + opt.label) +
("," + str(j + 1)) +
("," + pref) + "\n")
def main(opt):
logging.getLogger().setLevel(logging.DEBUG if opt.v else logging.INFO)
base_dict = dict(t_path=opt.t_path,
lazy_wl=opt.lazy_wl,
sada=False,
space_usage=False,
time_usage=False,
answer=True,
load_cst=opt.load_cst,
runs_progress=opt.runs_progress,
ms_progress=opt.ms_progress)
base_dir = os.path.dirname(opt.t_path)
out_paths = []
for i, s_path in enumerate(
glob.glob(base_dir + "/" + opt.species + "*.juststring")):
out_path = "%s__%s" % (opt.t_path.replace(".juststring", ""),
os.path.basename(
s_path.replace(".juststring", "")))
command = MsInterface.ms_command_from_dict(
dict(s_path=s_path, out_path=out_path, **base_dict))
print command
res = get_output(command)
if j == 0:
fd.write(res[0] + "," + header_suff + "\n")
for line in res[1:]:
fd.write(line.replace(" ", "") +
("," + opt.label) +
("," + str(j + 1)) +
("," + pref) + "\n")
if __name__ == "__main__":
arg_parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
epilog="Olgert Denas ([email protected])")
for k in MsInterface.params:
args, kwargs = MsInterface.as_argparse_kwds(k)
arg_parser.add_argument(*args, **kwargs)
verbose_args(arg_parser)
arg_parser.add_argument("--repeat", type=int, default=1,
help="repeat experiment")
arg_parser.add_argument("--label", type=str, default='default',
help="ad a label column to output")
arg_parser.add_argument("--repeat_colname", type=str, default='ntrial',
help="col label corresponding to the repeat nr.")
arg_parser.add_argument("--output", type=str, default='/dev/stdout',
help="output")
sys.exit(main(arg_parser.parse_args()))
def main(opt):
logging.getLogger().setLevel(logging.DEBUG if opt.v else logging.INFO)
LG.debug("running on S=%s, T=%s", opt.s_path, opt.t_path)
command = MsInterface.ms_command_from_dict(vars(opt))
LG.debug("running: " + str(command))
subprocess.check_call(command, shell=True)