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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 layout(args):
 """ %prog layout omgfile taxa Build column formatted gene lists after omgparse(). Use species list separated by comma in place of taxa, e.g. "BR,BO,AN,CN" """

    p = OptionParser(layout.__doc__)
    p.add_option("--sort",
                 help="Sort layout file based on bedfile [default: %default]")
    opts, args = p.parse_args(args)

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

    omgfile, taxa = args
    listfile = omgfile.rsplit(".", 1)[0] + ".list"
    taxa = taxa.split(",")
    ntaxa = len(taxa)
    fw = open(listfile, "w")

    data = []
    fp = open(omgfile)
    for row in fp:
        genes, idxs = row.split()
        row = ["."] * ntaxa
        genes = genes.split(",")
        ixs = [int(x) for x in idxs.split(",")]
        for gene, idx in zip(genes, ixs):
            row[idx] = gene
        txs = ",".join(taxa[x] for x in ixs)
        print("\t".join(("\t".join(row), txs)), file=fw)
        data.append(row)

    coldata = zip(*data)
    ngenes = []
    for i, tx in enumerate(taxa):
        genes = [x for x in coldata[i] if x != '.']
        genes = set(x.strip("|") for x in genes)
        ngenes.append((len(genes), tx))

    details = ", ".join("{0} {1}".format(a, b) for a, b in ngenes)
    total = sum(a for a, b in ngenes)
    s = "A list of {0} orthologous families that collectively".format(len(data))
    s += " contain a total of {0} genes ({1})".format(total, details)
    print(s, file=sys.stderr)

    fw.close()
    lastcolumn = ntaxa + 1
    cmd = "sort -k{0},{0} {1} -o {1}".format(lastcolumn, listfile)
    sh(cmd)

    logging.debug("List file written to `{0}`.".format(listfile))
    sort = opts.sort
    if sort:
        thread = Bed(sort)
        sort_layout(thread, listfile)