def pairs(args):
    """
    %prog pairs folder reference.fasta

    Estimate insert size distribution. Compatible with a variety of aligners,
    including BOWTIE and BWA.
    """
    p = OptionParser(pairs.__doc__)
    p.set_firstN()
    p.set_mates()
    p.set_aligner()
    opts, args = p.parse_args(args)

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

    cwd = os.getcwd()
    aligner = opts.aligner
    work = "-".join(("pairs", aligner))
    mkdir(work)

    from jcvi.formats.sam import pairs as ps
    if aligner == "bowtie":
        from jcvi.apps.bowtie import align
    elif aligner == "bwa":
        from jcvi.apps.bwa import align

    folder, ref = args
    ref = get_abs_path(ref)
    messages = []
    for p, prefix in iter_project(folder):
        samplefq = op.join(work, prefix + ".first.fastq")
        first([str(opts.firstN)] + p + ["-o", samplefq])

        os.chdir(work)
        align_args = [ref, op.basename(samplefq)]
        outfile, logfile = align(align_args)
        bedfile, stats = ps([outfile, "--rclip={0}".format(opts.rclip)])
        os.chdir(cwd)

        median = stats.median
        tag = "MP" if median > 1000 else "PE"
        median = str(median)
        pf, sf = median[:2], median[2:]
        if sf and int(sf) != 0:
            pf = str(int(pf) + 1)  # Get the first two effective digits
        lib = "{0}-{1}".format(tag, pf + '0' * len(sf))
        for i, xp in enumerate(p):
            suffix = "fastq.gz" if xp.endswith(".gz") else "fastq"
            link = "{0}-{1}.{2}.{3}".format(lib, prefix.replace("-", ""),
                                            i + 1, suffix)
            m = "\t".join(str(x) for x in (xp, link))
            messages.append(m)

    messages = "\n".join(messages)
    write_file("f.meta", messages, tee=True)
dataset/ETHPy150Open tanghaibao/jcvi/assembly/automaton.py/pairs/original