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,
"=======================================================================")
core.logCheck(l, logfilename, "\t\t\tMasking alignments with GBlocks")
core.logCheck(l, logfilename, "\t\t\t" + core.getDateTime())
if fileflag == 1:
core.logCheck(l, logfilename,
"INPUT | Masking alignment from file: " + ins)
else:
core.logCheck(l, logfilename,
"INPUT | Masking alignments from all files in: " + indir)
core.logCheck(l, logfilename, "INFO | GBlocks path set to: " + gb_path)
core.logCheck(l, logfilename, "INFO | Sequence type set to: " + seqtype)
if m == 1:
core.logCheck(
l, logfilename,
"INFO | Only accepting alignments with < 20% of sequence masked (for tree making)."
else:
script_outdir = script_outdir + "-" + outdir_suffix + "/";
outdir = script_outdir + "codeml_out/";
filelist = os.listdir(indir);
if aopt == 1:
ancdir = script_outdir + "anc_seqs_fa/";
print core.getTime() + " | Creating main output directory:\t" + script_outdir;
os.system("mkdir " + script_outdir);
logfilename = script_outdir + "run_codeml.log";
logfile = open(logfilename, "w");
logfile.write("");
logfile.close();
core.logCheck(l, logfilename, "=======================================================================");
core.logCheck(l, logfilename, "\t\t\tRunning codeml");
core.logCheck(l, logfilename, "\t\t\t" + core.getDateTime());
if fileflag == 1:
core.logCheck(l, logfilename, "INPUT | Making tree from file:\t\t" + ins);
else:
core.logCheck(l, logfilename, "INPUT | Running codeml on all files in:\t" + indir);
core.logCheck(l, logfilename, "INFO | PAML path set to:\t\t\t" + ppath);
if treefile != "":
core.logCheck(l, logfilename, "INFO | Using tree from file:\t\t" + treefile);
else:
core.logCheck(l, logfilename, "INFO | No tree file specified. codeml will infer a tree for each gene.");
if prune == 1:
core.logCheck(l, logfilename, "INFO | Pruning the tree for each gene.");
if bsopt == 0:
core.logCheck(l, logfilename, "INFO | Not doing branch-site test.");
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, "=======================================================================");
core.logCheck(l, logfilename, "\t\t\tMasking alignments with GBlocks");
core.logCheck(l, logfilename, "\t\t\t" + core.getDateTime());
if fileflag == 1:
core.logCheck(l, logfilename, "INPUT | Masking alignment from file: " + ins);
else:
core.logCheck(l, logfilename, "INPUT | Masking alignments from all files in: " + indir);
core.logCheck(l, logfilename, "INFO | GBlocks path set to: " + gb_path);
core.logCheck(l, logfilename, "INFO | Sequence type set to: " + seqtype);
if m == 1:
core.logCheck(l, logfilename, "INFO | Only accepting alignments with < 20% of sequence masked (for tree making).");
else:
core.logCheck(l, logfilename, "INFO | Using default GBlocks settings (stringent).");
if v == 1:
core.logCheck(l, logfilename, "INFO | Printing all GBlocks output to the screen.");
else:
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
os.system("mkdir '" + script_outdir + "'")
logfilename = script_outdir + "supertreemaker.log"
logfile = open(logfilename, "w")
logfile.write("")
logfile.close()
##Pre-run prep: creating log files and output directories, etc...
core.logCheck(
l, logfilename,
"=======================================================================")
core.logCheck(l, logfilename,
"\tSupertree making with SDM, R, newickutils, and r8s")
core.logCheck(l, logfilename, "\t\t\t" + core.getDateTime())
core.logCheck(l, logfilename,
"INPUT | Making tree from file:\t\t\t" + infilename)
core.logCheck(l, logfilename,
"INPUT | Input file located in:\t\t\t" + indir)
if njopt == 1:
core.logCheck(
l, logfilename,
"INFO | Using Average Consensus method in SDM to build distance matrix."
)
core.logCheck(
l, logfilename,
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
mk_cmd = "mkdir " + script_outdir
os.system(mk_cmd)
logfilename = os.path.join(script_outdir, "run_codeml.log")
# logfile = open(logfilename, "w");
# logfile.write("");
# logfile.close();
core.logCheck(
l, logfilename,
"=======================================================================")
core.logCheck(l, logfilename, "\t\t\tRunning codeml")
core.logCheck(l, logfilename, "\t\t\t" + core.getDateTime())
if fileflag == 1:
core.logCheck(l, logfilename,
"INPUT | Making tree from file:\t\t" + ins)
else:
core.logCheck(l, logfilename,
"INPUT | Running codeml on all files in:\t" + indir)
core.logCheck(l, logfilename, "INFO | PAML path set to:\t\t\t" + ppath)
if treefile != "":
core.logCheck(l, logfilename,
"INFO | Using tree from file:\t\t" + treefile)
else:
core.logCheck(
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;
os.system("mkdir '" + script_outdir + "'");
logfilename = script_outdir + "supertreemaker.log";
logfile = open(logfilename, "w");
logfile.write("");
logfile.close();
##Pre-run prep: creating log files and output directories, etc...
core.logCheck(l, logfilename, "=======================================================================");
core.logCheck(l, logfilename, "\tSupertree making with SDM, R, newickutils, and r8s");
core.logCheck(l, logfilename, "\t\t\t" + core.getDateTime());
core.logCheck(l, logfilename, "INPUT | Making tree from file:\t\t\t" + infilename);
core.logCheck(l, logfilename, "INPUT | Input file located in:\t\t\t" + indir);
if njopt == 1:
core.logCheck(l, logfilename, "INFO | Using Average Consensus method in SDM to build distance matrix.");
core.logCheck(l, logfilename, "INFO | Using R to build a neighbor-joining tree from matrix.");
else:
core.logCheck(l, logfilename, "INFO | Not creating consensus tree.");
if rr == 1:
core.logCheck(l, logfilename, "INFO | Rooting the NJ tree with species:\t\t" + outgroup);
if d == 0:
core.logCheck(l, logfilename, "INFO | NOT estimating divergence times with r8s.");
else:
core.logCheck(l, logfilename, "INFO | Will estimate divergence times with r8s.");
fileflag = 0
filelist = os.listdir(ins)
ins = os.path.abspath(ins)
script_outdir = os.path.abspath(script_outdir)
bestdir = os.path.join(script_outdir, "raxml-best")
outdir = os.path.join(script_outdir, "raxml-out")
print core.getTime() + " | Creating main output directory:\t" + script_outdir
os.system("mkdir '" + script_outdir + "'")
logfilename = os.path.join(script_outdir, "run_raxml.log")
core.filePrep(logfilename)
core.logCheck(
l, logfilename,
"=======================================================================")
core.logCheck(l, logfilename, "\t\t\tBuilding trees with RAxML")
core.logCheck(l, logfilename, "\t\t\t" + core.getDateTime())
if fileflag == 1:
core.logCheck(l, logfilename,
"INPUT | Making tree from file:\t\t" + ins)
else:
core.logCheck(l, logfilename,
"INPUT | Making trees from all files in:\t" + ins)
core.logCheck(l, logfilename, "INPUT | RAxML path set to:\t\t\t" + rax_path)
core.logCheck(l, logfilename,
"INFO | Using the following DNA or AA model:\t" + model)
if b > 0:
core.logCheck(
l, logfilename,
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")
logfile.write("")
logfile.close()
core.logCheck(l, logfilename, "=======================================================================")
core.logCheck(l, logfilename, "\t\t\tBuilding trees with RAxML")
core.logCheck(l, logfilename, "\t\t\t" + core.getDateTime())
if fileflag == 1:
core.logCheck(l, logfilename, "INPUT | Making tree from file:\t\t" + indir)
else:
core.logCheck(l, logfilename, "INPUT | Making trees from all files in:\t" + indir)
core.logCheck(l, logfilename, "INPUT | RAxML path set to:\t\t\t" + rax_path)
core.logCheck(l, logfilename, "INFO | Using the following DNA or AA model:\t" + model)
if b > 0:
core.logCheck(l, logfilename, "INFO | Performing " + str(b) + " bootstrap replicates per tree.")
else:
core.logCheck(l, logfilename, "INFO | Not performing bootstrap analysis.")
if t > 1:
core.logCheck(l, logfilename, "INFO | Using " + str(t) + " threads.")
else: