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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 setup_and_run_bwakit(job, uuid, url, rg_line, config, paired_url=None):
 """ Downloads and runs bwakit for BAM or FASTQ files :param JobFunctionWrappingJob job: passed automatically by Toil :param str uuid: Unique sample identifier :param str url: FASTQ or BAM file URL. BAM alignment URL must have .bam extension. :param Namespace config: Input parameters and shared FileStoreIDs Requires the following config attributes: config.genome_fasta FilesStoreID for reference genome fasta file config.genome_fai FilesStoreID for reference genome fasta index file config.cores Number of cores for each job config.trim If True, trim adapters using bwakit config.amb FileStoreID for BWA index file prefix.amb config.ann FileStoreID for BWA index file prefix.ann config.bwt FileStoreID for BWA index file prefix.bwt config.pac FileStoreID for BWA index file prefix.pac config.sa FileStoreID for BWA index file prefix.sa config.alt FileStoreID for alternate contigs file or None :param str|None paired_url: URL to paired FASTQ :param str|None rg_line: Read group line (i.e. @RG\tID:foo\tSM:bar) :return: BAM FileStoreID :rtype: str """

    bwa_config = deepcopy(config)
    bwa_config.uuid = uuid
    bwa_config.rg_line = rg_line

    # bwa_alignment uses a different naming convention
    bwa_config.ref = config.genome_fasta
    bwa_config.fai = config.genome_fai

    # Determine if sample is a FASTQ or BAM file using the file extension
    basename, ext = os.path.splitext(url)
    ext = ext.lower()
    if ext == '.gz':
        _, ext = os.path.splitext(basename)
        ext = ext.lower()

    # The pipeline currently supports FASTQ and BAM files
    require(ext in ['.fq', '.fastq', '.bam'],
            'Please use .fq or .bam file extensions:\n%s' % url)

    # Download fastq files
    samples = []
    input1 = job.addChildJobFn(download_url_job,
                               url,
                               name='file1',
                               s3_key_path=config.ssec,
                               disk=config.file_size)

    samples.append(input1.rv())

    # If the extension is for a BAM  file, then configure bwakit to realign the BAM file.
    if ext == '.bam':
        bwa_config.bam = input1.rv()
    else:
        bwa_config.r1 = input1.rv()

    # Download the paired FASTQ URL
    if paired_url:
        input2 = job.addChildJobFn(download_url_job,
                                   paired_url,
                                   name='file2',
                                   s3_key_path=config.ssec,
                                   disk=config.file_size)
        samples.append(input2.rv())
        bwa_config.r2 = input2.rv()

    # The bwakit disk requirement depends on the size of the input files and the index
    # Take the sum of the input files and scale it by a factor of 4
    bwa_index_size = sum([getattr(config, index_file).size
                          for index_file in ['amb', 'ann', 'bwt', 'pac', 'sa', 'alt']
                          if getattr(config, index_file, None) is not None])

    bwakit_disk = PromisedRequirement(lambda lst, index_size:
                                      int(4 * sum(x.size for x in lst) + index_size),
                                      samples,
                                      bwa_index_size)

    return job.addFollowOnJobFn(run_bwakit,
                                bwa_config,
                                sort=False,         # BAM files are sorted later in the pipeline
                                trim=config.trim,
                                cores=config.cores,
                                disk=bwakit_disk).rv()