return args.input, args.target_specs, args.output_suffix;
elif errorflag == 1:
parser.print_help();
sys.exit();
############################################
#Main Block
############################################
starttime = gwctcore.getLogTime();
indir, targets, suffix = optParse(0);
targets = targets.split(",");
indir, script_outdir = gwctcore.getOutdir(indir, "gwct", starttime, suffix);
print "# " + gwctcore.getTime() + " | Creating main output directory:\t" + script_outdir;
os.system("mkdir " + script_outdir);
logfilename = os.path.join(script_outdir, "gwct.log");
logfile = open(logfilename, "w");
logfile.write("");
logfile.close();
uniq_header = "#\tChromosome\tGeneID\tAlignLen\tPosition\tBackgroundAlleles\tTargetAlleles\n";
l = 1;
sp = 65;
gwctcore.logCheck(l, logfilename, "# =======================================================================");
gwctcore.logCheck(l, logfilename, "#\tGWCT: Genome-Wide Convergence Tester -- Unique substitutions");
gwctcore.logCheck(l, logfilename, "#\t\t\t" + gwctcore.getDateTime());
############################################
#Main Block
############################################
ins, ppath, treefile, prune, seqtype, bsopt, aopt, v, l, outdir_suffix = optParse(0);
starttime = gwctcore.getLogTime();
if not os.path.isdir(ppath):
gwctcore.errorOut(10, "-c must be a valid directory path");
optParse(1);
if os.path.isfile(ins):
fileflag = 1;
indir = os.path.dirname(os.path.realpath(ins));
indir, script_outdir = gwctcore.getOutdir(indir, "run_codeml", starttime, outdir_suffix);
outdir = os.path.join(script_outdir, "codeml_out");
if aopt == 1:
ancdir = os.path.join(script_outdir, "anc_seqs_fa");
filelist = [ins];
else:
fileflag = 0;
indir, script_outdir = gwctcore.getOutdir(ins, "run_codeml", starttime, outdir_suffix);
outdir = os.path.join(script_outdir, "codeml_out");
filelist = os.listdir(indir);
if aopt == 1:
ancdir = os.path.join(script_outdir, "anc_seqs_fa");
print gwctcore.getTime() + " | Creating main output directory:\t" + script_outdir;
os.system("mkdir " + script_outdir);
return args.input, args.target_specs, args.output_suffix
elif errorflag == 1:
parser.print_help()
sys.exit()
############################################
#Main Block
############################################
starttime = gwctcore.getLogTime()
indir, targets, suffix = optParse(0)
targets = targets.split(",")
indir, script_outdir = gwctcore.getOutdir(indir, "gwct", starttime, suffix)
print "# " + gwctcore.getTime(
) + " | Creating main output directory:\t" + script_outdir
os.system("mkdir " + script_outdir)
logfilename = os.path.join(script_outdir, "gwct.log")
logfile = open(logfilename, "w")
logfile.write("")
logfile.close()
uniq_header = "#\tChromosome\tGeneID\tAlignLen\tPosition\tBackgroundAlleles\tTargetAlleles\n"
l = 1
sp = 65
gwctcore.logCheck(
l, logfilename,
