def contamination(args):
    """
    %prog contamination folder Ecoli.fasta

    Remove contaminated reads. The FASTQ files in the folder will automatically
    pair and filtered against Ecoli.fasta to remove contaminants using BOWTIE2.
    """
    from jcvi.apps.bowtie import align

    p = OptionParser(contamination.__doc__)
    p.add_option("--mapped", default=False, action="store_true",
                 help="Retain contaminated reads instead [default: %default]")
    p.set_cutoff(cutoff=800)
    p.set_mateorientation(mateorientation="+-")
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    folder, ecoli = args
    ecoli = get_abs_path(ecoli)
    tag = "--mapped" if opts.mapped else "--unmapped"
    for p, pf in iter_project(folder):
        align_opts = [ecoli] + p + [tag]
        align_opts += ["--cutoff={0}".format(opts.cutoff), "--null"]
        if opts.mateorientation:
            align_opts += ["--mateorientation={0}".format(opts.mateorientation)]
        samfile, logfile = align(align_opts)
dataset/ETHPy150Open tanghaibao/jcvi/assembly/automaton.py/contamination/original