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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 _target_chroms_and_header(bam_file, data):
 """Get a list of chromosomes to target and new updated ref_file header. Could potentially handle remapping from chr1 -> 1 but currently disabled due to speed issues. """

    special_remaps = {"chrM": "MT", "MT": "chrM"}
    target_chroms = dict([(x.name, i) for i, x in enumerate(ref.file_contigs(dd.get_ref_file(data)))
                          if chromhacks.is_autosomal_or_sex(x.name)])
    out_chroms = []
    with pysam.Samfile(bam_file, "rb") as bamfile:
        for bami, bam_contig in enumerate([c["SN"] for c in bamfile.header["SQ"]]):
            if bam_contig in target_chroms:
                target_chrom = bam_contig
            elif bam_contig in special_remaps and special_remaps[bam_contig] in target_chroms:
                target_chrom = special_remaps[bam_contig]
            elif bam_contig.startswith("chr") and bam_contig.replace("chr", "") in target_chroms:
                target_chrom = bam_contig.replace("chr", "")
            elif "chr%s" % bam_contig in target_chroms:
                target_chrom = "chr%s" % bam_contig
            else:
                target_chrom = None
            # target_chrom == bam_contig ensures we don't try chr1 -> 1 style remapping
            if target_chrom and target_chrom == bam_contig:
                # Order not required if dealing with SAM file header fixing
                #assert bami == target_chroms[target_chrom], \
                #    ("remove_extracontigs: Non-matching order of standard contig: %s %s (%s vs %s)" %
                #     (bam_file, target_chrom, bami, target_chroms[target_chrom]))
                out_chroms.append(target_chrom)
    assert out_chroms, ("remove_extracontigs: Did not find any chromosomes in reference file: %s %s" %
                        (bam_file, target_chroms))
    return out_chroms