optParse(1)
return args.input, args.gblocks_path, st, args.run_mode, args.verbosity, args.log_opt
elif errorflag == 1:
parser.print_help()
sys.exit()
############################################
#Main Block
############################################
ins, gb_path, seqtype, m, v, l = optParse(0)
starttime = core.getLogTime()
if os.path.isfile(ins):
fileflag = 1
indir = os.path.dirname(os.path.realpath(ins)) + "/"
indir, outdir = core.getOutdir(indir, "run_gblocks", starttime)
filelist = [ins]
else:
fileflag = 0
indir, outdir = core.getOutdir(ins, "run_gblocks", starttime)
filelist = os.listdir(indir)
print core.getTime() + " | Creating main output directory..."
os.system("mkdir " + outdir)
logfilename = outdir + "run_gblocks.log"
return args.input_file, args.r_output_file, args.nj_opt, args.nj_outgroup, args.reroot_opt, args.div_est_opt, args.r8s_output_file, args.num_sites, cal_specs, cal_age, args.log_opt, args.script_logdir, args.logdir_suffix
elif errorflag == 1:
parser.print_help()
sys.exit()
############################################
#Main Block
############################################
infilename, routfilename, njopt, outgroup, rr, d, r8soutfilename, numsites, calspec, calage, l, script_outdir_initial, outdir_suffix = optParse(
0)
starttime = core.getLogTime()
if infilename.find("/") != -1:
indir = os.path.dirname(os.path.realpath(infilename)) + "/"
infilename = infilename[infilename.rfind("/") + 1:]
else:
indir = os.getcwd() + "/"
indir, script_outdir = core.getOutdir(indir, "supertreemaker", starttime)
print script_outdir
print os.path.basename(os.path.normpath(script_outdir))
if script_outdir_initial != None:
if not os.path.isdir(script_outdir_initial):
core.errorOut(8, "-z must be a valid directory")
optParse(1)
core.errorOut(4, "-l must take values of either 1 or 0");
optParse(1);
return args.input, args.gblocks_path, st, args.run_mode, args.verbosity, args.log_opt;
elif errorflag == 1:
parser.print_help();
sys.exit();
############################################
#Main Block
############################################
ins, gb_path, seqtype, m, v, l = optParse(0);
starttime = core.getLogTime();
if os.path.isfile(ins):
fileflag = 1;
indir = os.path.dirname(os.path.realpath(ins)) + "/";
indir, outdir = core.getOutdir(indir, "run_gblocks", starttime);
filelist = [ins];
else:
fileflag = 0;
indir, outdir = core.getOutdir(ins, "run_gblocks", starttime);
filelist = os.listdir(indir);
print core.getTime() + " | Creating main output directory...";
os.system("mkdir " + outdir);
logfilename = outdir + "run_gblocks.log";
core.errorOut(7, "-l must take values of either 1 or 0");
optParse(1);
return args.input_file, args.r_output_file, args.nj_opt, args.nj_outgroup, args.reroot_opt, args.div_est_opt, args.r8s_output_file, args.num_sites, cal_specs, cal_age, args.log_opt, args.script_logdir, args.logdir_suffix;
elif errorflag == 1:
parser.print_help();
sys.exit();
############################################
#Main Block
############################################
infilename, routfilename, njopt, outgroup, rr, d, r8soutfilename, numsites, calspec, calage, l, script_outdir_initial, outdir_suffix = optParse(0);
starttime = core.getLogTime();
if infilename.find("/") != -1:
indir = os.path.dirname(os.path.realpath(infilename)) + "/";
infilename = infilename[infilename.rfind("/")+1:];
else:
indir = os.getcwd() + "/";
indir, script_outdir = core.getOutdir(indir, "supertreemaker", starttime);
print script_outdir;
print os.path.basename(os.path.normpath(script_outdir));
if script_outdir_initial != None:
if not os.path.isdir(script_outdir_initial):
core.errorOut(8, "-z must be a valid directory");
optParse(1);
