def spades(args):
    """
    %prog spades folder

    Run automated SPADES.
    """
    from jcvi.formats.fastq import readlen

    p = OptionParser(spades.__doc__)
    opts, args = p.parse_args(args)

    if len(args) == 0:
        sys.exit(not p.print_help())

    folder, = args
    for p, pf in iter_project(folder):
        rl = readlen([p[0], "--silent"])

        # <http://spades.bioinf.spbau.ru/release3.1.0/manual.html#sec3.4>
        kmers = None
        if rl >= 150:
            kmers = "21,33,55,77"
        elif rl >= 250:
            kmers = "21,33,55,77,99,127"

        cmd = "spades.py"
        if kmers:
            cmd += " -k {0}".format(kmers)
        cmd += " --careful"
        cmd += " --pe1-1 {0} --pe1-2 {1}".format(*p)
        cmd += " -o {0}_spades".format(pf)
        print cmd
dataset/ETHPy150Open tanghaibao/jcvi/assembly/automaton.py/spades/original