input="allele.table",
name="BS.%d" %bs))
condor_temp = main + "\n".join(a)
out = open(os.path.join(outpath, "condor.st"), "w")
out.write(condor_temp)
out.close()
if __name__ == '__main__':
outdir = sys.argv[1]
BS = int(sys.argv[2])
indir = sys.argv[3]
if (os.path.exists(outdir)):
#i = 0
#while os.path.exists(outdir+".back.%d" %i):
# i += 1
#os.rename(outdir, outdir+".back.%d"%i)
sys.stdout.writelines("The output directory %s already exists. Do you want to proceed? (y/n)?" % outdir)
a = sys.stdin.readline()
if a != "y\n":
sys.exit(1)
else:
os.makedirs(outdir)
require_dir(os.path.join(outdir, "logs"))
make_BS_condor(outdir, BS, indir)
make_ST_condor(outdir, "mpest", "", "mpest", BS)
sys.stdout.writelines(
"The output directory %s already exists. Do you want to proceed? (y/n)?"
% outdir)
a = sys.stdin.readline()
if a != "y\n":
sys.exit(1)
else:
os.makedirs(outdir)
for ds in datasets:
ds_paths, replicas, names, outgroup = get_datasets(
ds, twophase_conf.get("datasets", ds))
for ds_path in ds_paths:
ds_name = os.path.basename(ds_path)
out_ds_path = os.path.join(outdir, ds_name)
require_dir(out_ds_path)
for rep in replicas:
out_rep_path = os.path.join(out_ds_path, "R%d" % rep)
print out_rep_path
require_dir(out_rep_path)
for ml in mltools:
ml_tool = ml.split(".")[0]
for alg in algtools:
out_path = os.path.join(out_rep_path,
"%s_%s" % (ml, alg))
require_dir(out_path)
require_dir(os.path.join(out_path, "logs"))
alg_tool = alg.split(".")[0]
sys.stdout.writelines(
"The output directory %s already exists. Do you want to proceed? (y/n)?"
% outdir)
a = sys.stdin.readline()
if a != "y\n":
sys.exit(1)
else:
os.makedirs(outdir)
for ds in datasets:
ds_paths, replicas, names, outgroup, options = get_datasets(
ds, twophase_conf.get("datasets", ds))
for ds_path in ds_paths:
ds_name = os.path.basename(ds_path)
out_ds_path = os.path.join(outdir, ds_name)
require_dir(out_ds_path)
for rep in replicas:
out_rep_path = os.path.join(out_ds_path, "R%d" % rep)
print out_rep_path
require_dir(out_rep_path)
for ml in mltools:
ml_tool = ml.split(".")[0]
for alg in algtools:
out_path = os.path.join(out_rep_path,
"%s_%s" % (ml, alg))
require_dir(out_path)
require_dir(os.path.join(out_path, "logs"))
alg_tool = alg.split(".")[0]