targets = [[t] for t in targets]
print targets
results_dict = convergence.convCheck(infilename, results_dict,
node_key, targets,
prob_thresh, gid,
tree_dict, pairwise)
return results_dict
############################################
#Main Block
############################################
starttime = gc.getLogTime()
indir, orig_targets, pairwise, prob_thresh, num_threads, output = optParse()
if platform.system() == "Windows" and num_threads != 1:
print "\n** Warning! Multi-processing not currently supported on Windows. Switching to serial version (1 process).\n"
num_threads = 1
outdir = gc.defaultOut(output, indir, "-gwct")
print gc.getTime() + " | + Creating main output directory:\t" + outdir
os.system("mkdir " + outdir)
ancdir = os.path.join(indir, "anc-seqs-fa")
if not os.path.isdir(ancdir):
ancdir = os.path.join(indir, "anc_seqs_fa")
if not os.path.isdir(ancdir):
sys.exit(
##### #def core.logCheck(lopt, lfilename, outline): # if lopt == 1: # core.printWrite(lfilename, outline); # else: # print outline; ############################################ #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:
if args.target_specs == None:
gwctcore.errorOut(2, "-t must be defined");
optParse(1);
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;
if n == targets[0]:
node_key = node_key + "-";
if node_key not in results_dict:
results_dict[node_key] = [[],[],[]];
results_dict = convergence.convCheck(infilename, results_dict, node_key, targets, prob_thresh, chromosome, gene, tree_dict, u);
return results_dict;
############################################
#Main Block
############################################
starttime = gwctcore.getLogTime();
indir, orig_targets, unique, pairwise, prob_thresh, num_threads, suffix = optParse(0);
if suffix != "":
suffix = "-" + suffix;
if sys.platform.find("win") != -1 and sys.platform != "darwin":
rm_cmd = "del ";
else:
rm_cmd = "rm ";
indir, script_outdir = gwctcore.getOutdir(indir, "gwct", starttime, suffix);
print indir;
inslist = os.listdir(indir);
if unique != 1:
for each in inslist:
if each.find("run_codeml") != -1 or each.find("codeml_combined") != -1:
try:
td, tree, r = gt.treeParse(open(args.tree_file, "r").read().replace("\n",""));
except:
sys.exit(gc.errorOut(4, "-t does not contain a valid Newick string!"));
if args.verbosity not in [0,1]:
sys.exit(gc.errorOut(6, "-v must take values of either 1 or 0"));
return args.input, args.paml_path, args.tree_file, args.prune_opt, args.verbosity, args.output;
############################################
# Main Block
############################################
starttime = gc.getLogTime();
indir, path, treefile, prune, v, output = optParse();
# Get input options.
file_flag = 0;
outdir = gc.defaultOut(output, indir, "-gwct-codeml");
print "+ Creating main output directory:\t" + outdir;
os.system("mkdir " + outdir);
codemldir = os.path.join(outdir, "codeml-out");
ancdir = os.path.join(outdir, "anc-seqs-fa");
logfilename = os.path.join(outdir, "gwct-codeml.log");
# Set output file and directory info.
gc.printWrite(logfilename, "Program call: " + " ".join(sys.argv));
pad = 50;
if args.target_specs == None:
gwctcore.errorOut(2, "-t must be defined")
optParse(1)
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
if node_key not in results_dict:
results_dict[node_key] = [[], [], []]
results_dict = convergence.convCheck(infilename, results_dict,
node_key, targets,
prob_thresh, chromosome,
gene, tree_dict, u)
return results_dict
############################################
#Main Block
############################################
starttime = gwctcore.getLogTime()
indir, orig_targets, unique, pairwise, prob_thresh, num_threads, suffix = optParse(
0)
if suffix != "":
suffix = "-" + suffix
if sys.platform.find("win") != -1 and sys.platform != "darwin":
rm_cmd = "del "
else:
rm_cmd = "rm "
indir, script_outdir = gwctcore.getOutdir(indir, "gwct", starttime, suffix)
print indir
inslist = os.listdir(indir)
if unique != 1:
for each in inslist:
