def at(path, step, branch, isdir, step_choices):
if not isdir:
checkstep(step, step_choices)
if branch is not None:
for b in branch:
fishfiles = TollCheck(path=path, step=step, branch=b)
fishfiles.massiveaddition(isdir=isdir)
else:
fishfiles = TollCheck(path=path, step=step, branch=branch)
fishfiles.massiveaddition(isdir=isdir)
def main():
args = getOpts()
tc_class = TollCheck(path=args.path, step="step6b", req_merge=True)
preAln(tc_class=tc_class,
threads=args.threads,
flank=True,
otophysi=False,
pattern=args.fasta).create_files()
tc_class.massiveaddition()
def main():
args = getOpts()
tc_class = TollCheck(path=args.path, step="step6macse", branch=args.branch)
macse(tc_class=tc_class,
suffix=args.suffix,
homovalue=args.min_homo,
otophysi=False,
memory=int((args.memory * 1024) / args.threads),
threads=args.threads,
keep=args.keepdb).run()
tc_class.massiveaddition()
