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"
logfile = open(logfilename, "w")
logfile.write("")
logfile.close()
core.logCheck(
############################################ ins, ppath, treefile, prune, seqtype, bsopt, aopt, v, l, outdir_suffix = optParse(0); starttime = core.getLogTime(); if not os.path.isdir(ppath): core.errorOut(10, "-c must be a valid directory path"); optParse(1); elif ppath[-1] != "/": ppath = ppath + "/"; if os.path.isfile(ins): fileflag = 1; indir = os.path.dirname(os.path.realpath(ins)) + "/"; indir, script_outdir = core.getOutdir(indir, "run_codeml", starttime); outdir = script_outdir + "codeml_out/"; if aopt == 1: ancdir = script_outdir + "anc_seqs_fa/"; filelist = [ins]; else: fileflag = 0; indir, script_outdir = core.getOutdir(ins, "run_codeml", starttime); if outdir_suffix != None: if script_outdir[-1] == "/": script_outdir = script_outdir[:len(script_outdir)-1] + "-" + outdir_suffix + "/"; else: script_outdir = script_outdir + "-" + outdir_suffix + "/"; outdir = script_outdir + "codeml_out/"; filelist = os.listdir(indir);
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";
logfile = open(logfilename, "w");
logfile.write("");
logfile.close();
core.logCheck(l, logfilename, "=======================================================================");
############################################
#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)
script_outdir = os.path.join(
script_outdir_initial,
os.path.basename(os.path.normpath(script_outdir)))
if outdir_suffix != None:
if script_outdir[-1] == "/":
script_outdir = script_outdir[:len(script_outdir) -
1] + "-" + outdir_suffix + "/"
else:
ins, ppath, treefile, prune, seqtype, bsopt, aopt, v, l, outdir_suffix = optParse(
0)
starttime = core.getLogTime()
if not os.path.isdir(ppath):
core.errorOut(10, "-c must be a valid directory path")
optParse(1)
codeml_path = os.path.join(ppath, "bin", "codeml")
if outdir_suffix != "":
outdir_suffix = "-" + outdir_suffix
if os.path.isfile(ins):
fileflag = 1
indir = os.path.dirname(os.path.realpath(ins))
indir, script_outdir = core.getOutdir(indir, "run_codeml", starttime)
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 = core.getOutdir(ins, "run_codeml", outdir_suffix,
starttime)
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 core.getTime() + " | Creating main output directory:\t" + script_outdir
############################################
#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);
script_outdir = os.path.join(script_outdir_initial, os.path.basename(os.path.normpath(script_outdir)));
if outdir_suffix != None:
if script_outdir[-1] == "/":
script_outdir = script_outdir[:len(script_outdir)-1] + "-" + outdir_suffix + "/";
else:
script_outdir = script_outdir + "-" + outdir_suffix + "/";
print core.getTime() + " | Creating main output directory:\t" + script_outdir;
############################################
#Main Block
############################################
ins, rax_path, model, b, t, v, const_tree, bl_opt, script_outdir, l = optParse(
0)
starttime = core.getLogTime()
if script_outdir == "":
if os.path.isfile(ins):
fileflag = 1
indir = os.path.dirname(os.path.realpath(ins))
filelist = [os.path.abspath(ins)]
indir, script_outdir = core.getOutdir(indir, "run_raxml", starttime)
ins = indir
else:
fileflag = 0
indir, script_outdir = core.getOutdir(ins, "run_raxml", starttime)
filelist = os.listdir(indir)
ins = indir
else:
counter = 1
while os.path.exists(script_outdir):
if counter == 1:
script_outdir = script_outdir + "-" + str(counter)
else:
script_outdir = script_outdir[:script_outdir.index("-") +
1] + str(counter)
counter += 1
parser.print_help()
sys.exit()
############################################
# Main Block
############################################
ins, rax_path, model, b, t, v, c, l = optParse(0)
starttime = core.getLogTime()
if os.path.isfile(ins):
fileflag = 1
indir = os.path.dirname(os.path.realpath(ins)) + "/"
indir, script_outdir = core.getOutdir(indir, "run_raxml", starttime)
bestdir = script_outdir + "raxml_best/"
outdir = script_outdir + "raxml_out/"
filelist = [ins]
else:
fileflag = 0
indir, script_outdir = core.getOutdir(ins, "run_raxml", starttime)
bestdir = script_outdir + "raxml_best/"
outdir = script_outdir + "raxml_out/"
filelist = os.listdir(indir)
print core.getTime() + " | Creating main output directory:\t" + script_outdir
os.system("mkdir '" + script_outdir + "'")
logfilename = script_outdir + "run_raxml.log"
logfile = open(logfilename, "w")
