def novo(args):
    """
    %prog novo reads.fastq

    Reference-free tGBS pipeline v1.
    """
    from jcvi.assembly.kmer import jellyfish, histogram
    from jcvi.assembly.preprocess import diginorm
    from jcvi.formats.fasta import filter as fasta_filter, format
    from jcvi.apps.cdhit import filter as cdhit_filter

    p = OptionParser(novo.__doc__)
    p.add_option("--technology", choices=("illumina", "454", "iontorrent"),
                 default="iontorrent", help="Sequencing platform")
    p.set_depth(depth=50)
    p.set_align(pctid=96)
    p.set_home("cdhit", default="/usr/local/bin/")
    p.set_home("fiona", default="/usr/local/bin/")
    p.set_home("jellyfish", default="/usr/local/bin/")
    p.set_cpus()
    opts, args = p.parse_args(args)

    if len(args) != 1:
        sys.exit(not p.print_help())

    fastqfile, = args
    cpus = opts.cpus
    depth = opts.depth
    pf, sf = fastqfile.rsplit(".", 1)

    diginormfile = pf + ".diginorm." + sf
    if need_update(fastqfile, diginormfile):
        diginorm([fastqfile, "--single", "--depth={0}".format(depth)])
        keepabund = fastqfile + ".keep.abundfilt"
        sh("cp -s {0} {1}".format(keepabund, diginormfile))

    jf = pf + "-K23.histogram"
    if need_update(diginormfile, jf):
        jellyfish([diginormfile, "--prefix={0}".format(pf),
                    "--cpus={0}".format(cpus),
                    "--jellyfish_home={0}".format(opts.jellyfish_home)])

    genomesize = histogram([jf, pf, "23"])
    fiona = pf + ".fiona.fa"
    if need_update(diginormfile, fiona):
        cmd = op.join(opts.fiona_home, "fiona")
        cmd += " -g {0} -nt {1} --sequencing-technology {2}".\
                    format(genomesize, cpus, opts.technology)
        cmd += " -vv {0} {1}".format(diginormfile, fiona)
        logfile = pf + ".fiona.log"
        sh(cmd, outfile=logfile, errfile=logfile)

    dedup = "cdhit"
    pctid = opts.pctid
    cons = fiona + ".P{0}.{1}.consensus.fasta".format(pctid, dedup)
    if need_update(fiona, cons):
        deduplicate([fiona, "--consensus", "--reads",
                     "--pctid={0}".format(pctid),
                     "--cdhit_home={0}".format(opts.cdhit_home)])

    filteredfile = pf + ".filtered.fasta"
    if need_update(cons, filteredfile):
        covfile = pf + ".cov.fasta"
        cdhit_filter([cons, "--outfile={0}".format(covfile),
                      "--minsize={0}".format(5 / depth)])
        fasta_filter([covfile, "50", "--outfile={0}".format(filteredfile)])

    finalfile = pf + ".final.fasta"
    if need_update(filteredfile, finalfile):
        format([filteredfile, finalfile, "--sequential=replace",
                    "--prefix={0}_".format(pf)])
dataset/ETHPy150Open tanghaibao/jcvi/projects/tgbs.py/novo/swapped operands of `/`