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 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 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")