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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 install(args):
 """ %prog install patchers.bed patchers.fasta backbone.fasta alt.fasta Install patches into backbone, using sequences from alternative assembly. The patches sequences are generated via jcvi.assembly.patch.fill(). The output is a bedfile that can be converted to AGP using jcvi.formats.agp.frombed(). """

    from jcvi.apps.align import blast
    from jcvi.formats.fasta import SeqIO

    p = OptionParser(install.__doc__)
    p.set_rclip(rclip=1)
    p.add_option("--maxsize", default=300000, type="int",
            help="Maximum size of patchers to be replaced [default: %default]")
    p.add_option("--prefix", help="Prefix of the new object [default: %default]")
    p.add_option("--strict", default=False, action="store_true",
            help="Only update if replacement has no gaps [default: %default]")
    opts, args = p.parse_args(args)

    if len(args) != 4:
        sys.exit(not p.print_help())

    pbed, pfasta, bbfasta, altfasta = args
    maxsize = opts.maxsize  # Max DNA size to replace gap
    rclip = opts.rclip

    blastfile = blast([altfasta, pfasta,"--wordsize=100", "--pctid=99"])
    order = Bed(pbed).order
    beforebed, afterbed = blast_to_twobeds(blastfile, order, rclip=rclip,
                                           maxsize=maxsize)

    beforefasta = fastaFromBed(beforebed, bbfasta, name=True, stranded=True)
    afterfasta = fastaFromBed(afterbed, altfasta, name=True, stranded=True)

    # Exclude the replacements that contain more Ns than before
    ah = SeqIO.parse(beforefasta, "fasta")
    bh = SeqIO.parse(afterfasta, "fasta")
    count_Ns = lambda x: x.seq.count('n') + x.seq.count('N')
    exclude = set()
    for arec, brec in zip(ah, bh):
        an = count_Ns(arec)
        bn = count_Ns(brec)
        if opts.strict:
            if bn == 0:
                continue

        elif bn < an:
            continue

        id = arec.id
        exclude.add(id)

    logging.debug("Ignore {0} updates because of decreasing quality."\
                    .format(len(exclude)))


    abed = Bed(beforebed, sorted=False)
    bbed = Bed(afterbed, sorted=False)
    abed = [x for x in abed if x.accn not in exclude]
    bbed = [x for x in bbed if x.accn not in exclude]

    abedfile = "before.filtered.bed"
    bbedfile = "after.filtered.bed"
    afbed = Bed()
    afbed.extend(abed)
    bfbed = Bed()
    bfbed.extend(bbed)

    afbed.print_to_file(abedfile)
    bfbed.print_to_file(bbedfile)

    shuffle_twobeds(afbed, bfbed, bbfasta, prefix=opts.prefix)