Argparse

if __name__ == "__main__":
    import argparse
    from argparse import RawTextHelpFormatter
    parser = argparse.ArgumentParser(
        formatter_class=RawTextHelpFormatter,
        description="""Generate lists of commands for ChIP - Seq analysis.
            1) Commands to create intersects of peaks from different replicates
            2) Commands to get the coverage for these intersects.""",
        )
    parser.add_argument('--config-file', '-cf',
        required=True,
        type=str,
        help="YAML configuration file"
        )
    parser.add_argument('--intersects', '-i',
        required=False,
        type=str,
        help="Filename for the list of intersection commands.",
        )
    parser.add_argument('--coverage', '-c',
        required=False,
        type=str,
        help="Filename for the list of coverage commands.",
        default=None
        )
    parser.add_argument('--fold', '-f',
        required=False,
        action="store_true",
        help="If included, fold and log-fold coverage will be calculated for intersects.",
        )
    args=parser.parse_args()

    sample_config_file=args.config_file
    intersects_commands_filename=args.intersects
    coverage_commands_filename=args.coverage
    fold = args.fold

    chipseq_config=ChipSeqConfiguration(sample_config_file)

    if intersects_commands_filename:
        chipseq_config.writeIntersectCommands(intersects_commands_filename)

    if coverage_commands_filename:
        chipseq_config.writeCoverageCommands(coverage_commands_filename)

    if fold:
        chipseq_config.writeFoldChange()

if __name__ == "__main__":

    import argparse

    parser = argparse.ArgumentParser(
        description='Count kmers in fastq files',
        epilog="""Tip: You can use this to create your reference. For instance
            run on your reference geneome without the --reference (-r)
            flag"""
        )
    parser.add_argument('--sample', '-s',
        required=True,
        type=str,
        help="The sample fastq file"
        )
   parser.add_argument('--outfile', '-o',
        required=False,
        type=str,
        help="output file",
        default=None
        )
    parser.add_argument('--kmer-length', '-k',
        required=True,
        type=int,
        help="kmer length"
        )
    parser.add_argument('--reference', '-r',
        required=False,
        type=str,
        help="reference kmer count file for normalized counts",
        default=None
        )

    args = parser.parse_args()

    #sys.exit()

    sample = args.sample
    outfilename = args.outfile
    kmer_length = args.kmer_length
    ref_countfile = args.reference

    #print("sample " + sample)
    #print("kmer_length " + str(kmer_length))

    ### Count kmers
    kmer_counts = countKmers(
        samplefile=sample,
        kmer_length=kmer_length
    )

    ### create outfile object or leave as None
    if outfilename != None:
        outfile = open(outfilename, 'w')
    else:
        print("No outfile specified. Writing to stdout.")

    if ref_countfile == None:
        print("Did not get a reference file. Not normalizing.")
        printKmerCounts(
            sample_kmer_counts=kmer_counts,
            outfile=outfile
        )
    else:
        print("Got reference file " + ref_countfile + ". Normalizing")
        printNormalizedKmerCounts(
            sample_kmer_counts=kmer_counts,
            ref_countfile=ref_countfile,
            outfile=outfile
        )