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")