parsing_opts.py 文件源码

def parsing_transcript():
    parser = argparse.ArgumentParser(
        description="This script is designed for preparing transcripts annotation files."
    )
    parser.add_argument("-g","--gtf",dest="gtfFile",required=True,type=str,
                        help='Default, suitable for GENCODE and ENSEMBL GTF file, \
                              please refer: https://en.wikipedia.org/wiki/GENCODE, \
                              or using GTFupdate command to update your GTF file.')
    parser.add_argument("-f","--fasta",dest="genomeFasta",required=True,type=str,
                        help="The genome sequences file in fasta format.")
    parser.add_argument("-o","--out_dir",required=True,type=str,dest="out_dir",help="annotation directory name.")
    parser.add_argument('-V',"--version",action="version",version=__version__)
    args = parser.parse_args()

    if not os.path.exists(args.out_dir):
        try:
            os.mkdir(args.out_dir)
        except OSError as e:
            raise e

    if not os.path.exists(args.gtfFile):
        raise ValueError("Error, gtf file not found:%s.\n" % args.gtfFile)

    if not os.path.exists(args.genomeFasta):
        raise ValueError("Error, genomic fasta not found: %s\n" % args.genomeFata)

    return args