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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
 def patch(args):
 """ %prog patch reference.fasta reads.fasta Run PBJelly with reference and reads. """

    from jcvi.formats.base import write_file
    from jcvi.formats.fasta import format

    p = OptionParser(patch.__doc__)
    p.add_option("--cleanfasta", default=False, action="store_true",
                 help="Clean FASTA to remove description [default: %default]")
    p.add_option("--highqual", default=False, action="store_true",
                 help="Reads are of high quality [default: %default]")
    p.set_home("pbjelly")
    p.set_cpus()
    opts, args = p.parse_args(args)

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

    ref, reads = args
    cpus = opts.cpus
    cmd = op.join(opts.pbjelly_home, "setup.sh")
    setup = "source {0}".format(cmd)
    if not which("fakeQuals.py"):
        sh(setup)

    pf = ref.rsplit(".", 1)[0]
    pr, px = reads.rsplit(".", 1)
    # Remove description line
    if opts.cleanfasta:
        oref = pf + ".f.fasta"
        oreads = pr + ".f.fasta"
        format([ref, oref])
        format([reads, oreads])
        ref, reads = oref, oreads

    # Check if the FASTA has qual
    ref, refq = fake_quals(ref)
    convert_reads = not px in ("fq", "fastq", "txt")
    if convert_reads:
        reads, readsq = fake_quals(reads)
        readsfiles = " ".join((reads, readsq))
    else:
        readsfiles = reads

    # Make directory structure
    dref, dreads = "data/reference", "data/reads"
    cwd = os.getcwd()
    reference = op.join(cwd, "{0}/{1}".format(dref, ref))
    reads = op.join(cwd, "{0}/{1}".format(dreads, reads))
    if not op.exists(reference):
        sh("mkdir -p {0}".format(dref))
        sh("cp {0} {1}/".format(" ".join((ref, refq)), dref))
    if not op.exists(reads):
        sh("mkdir -p {0}".format(dreads))
        sh("cp {0} {1}/".format(readsfiles, dreads))

    outputDir = cwd
    p = Protocol(outputDir, reference, reads, highqual=opts.highqual)
    p.write_xml()

    # Build the pipeline
    runsh = [setup]
    for action in "setup|mapping|support|extraction".split("|"):
        runsh.append("Jelly.py {0} Protocol.xml".format(action))

    runsh.append('Jelly.py assembly Protocol.xml -x "--nproc={0}"'.format(cpus))
    runsh.append("Jelly.py output Protocol.xml")

    runfile = "run.sh"
    contents = "\n".join(runsh)
    write_file(runfile, contents)