Esempi in Python per ArgumentParserPlus

Esempio n. 1

File: gimsan_submit.py Progetto: pnpnpn/gimsan-py

    #defaults
    description = """
Submit GIMSAN job
"""


    epilog = """
Examples:

%(prog)s --conf=conf_examples/test_window_sampling.cfg -v
%(prog)s --conf=conf_examples/test_window_sampling.cfg -v --overwrite
%(prog)s --conf=conf_examples/test_window_sampling.cfg -v --overwrite --dryrun --skip-null
"""

    argp = ArgumentParserPlus(description=description, epilog=epilog)
    argp.add_argument('--conf', required=True, help="", dest="conf_file")
    argp.add_argument('--overwrite', action="store_true", help="")
    argp.add_argument('--skip-null', action="store_true", help="")
    argp.add_argument('--dryrun', action="store_true", help="")
    argp.add_argument('-v', '--verbose', action='store_true')
    args = argp.parse_args()

    import logging
    if args.verbose:
        log_level = logging.DEBUG
    else:
        log_level = logging.INFO

    simple_stream_logging(log_level)

Esempio n. 2

Stand-alone version of sample_from_GC_content_range. Construct null datasets based on GC-content percentages
This is particularly created for the GIMSAN application.

Default window size: 100 bp
Default GC-content bin size: 5%%
If --genome is not specified, Markov model is used to generate the nullset.
"""

    epilog = """
Examples:

%(prog)s --template=testdata/ABF1_YPD_mod.fasta --outdir=testnull --mode=markov
"""
    #iters, genome, output-dir, binsize, wndsize

    argp = ArgumentParserPlus(description=description, epilog=epilog)
    argp.add_argument('--mode',
                      required=True,
                      choices=['markov', 'window'],
                      help="Markov or window-sampling")
    argp.add_argument('--template', required=True, help="template FASTA file")
    argp.add_argument('--genome', help="genome FASTA file")
    argp.add_argument('--iters', help="", type=int, default=10)
    argp.add_argument('--outdir', help="", required=True)
    argp.add_argument('-v', '--verbose', action='store_true')
    args = argp.parse_args()

    import logging
    if args.verbose:
        log_level = logging.DEBUG
    else:

Esempio n. 3

File: nullset_generator.py Progetto: pnpnpn/gimsan-py

This is particularly created for the GIMSAN application.

Default window size: 100 bp
Default GC-content bin size: 5%%
If --genome is not specified, Markov model is used to generate the nullset.
""" 


    epilog = """
Examples:

%(prog)s --template=testdata/ABF1_YPD_mod.fasta --outdir=testnull --mode=markov
""" 
    #iters, genome, output-dir, binsize, wndsize

    argp = ArgumentParserPlus(description=description, epilog=epilog)
    argp.add_argument('--mode', required=True, choices=['markov', 'window'], help="Markov or window-sampling")
    argp.add_argument('--template', required=True, help="template FASTA file")
    argp.add_argument('--genome', help="genome FASTA file")
    argp.add_argument('--iters', help="", type=int, default=10)
    argp.add_argument('--outdir', help="", required=True)
    argp.add_argument('-v', '--verbose', action='store_true')
    args = argp.parse_args()

    import logging
    if args.verbose:
        log_level = logging.DEBUG
    else:
        log_level = logging.INFO

    simple_stream_logging(log_level)

Esempio n. 4

if __name__ == '__main__':
    benchmark = time_benchmark.Benchmark()

    #defaults
    description = """
Generate GIMSAN result
"""

    epilog = """
Examples:

%(prog)s --dir=testout -v
"""

    argp = ArgumentParserPlus(description=description, epilog=epilog)
    argp.add_argument('--dir',
                      required=True,
                      help="main output directory used with gimsan_submit.py")
    argp.add_argument('--overwrite', action="store_true", help="")
    argp.add_argument('--dryrun', action="store_true", help="")
    argp.add_argument('-v', '--verbose', action='store_true')
    args = argp.parse_args()

    import logging
    if args.verbose:
        log_level = logging.DEBUG
    else:
        log_level = logging.INFO

    simple_stream_logging(log_level)

Esempio n. 5

    benchmark = time_benchmark.Benchmark()

    #defaults
    description = """
Submit GIMSAN job
"""

    epilog = """
Examples:

%(prog)s --conf=conf_examples/test_window_sampling.cfg -v
%(prog)s --conf=conf_examples/test_window_sampling.cfg -v --overwrite
%(prog)s --conf=conf_examples/test_window_sampling.cfg -v --overwrite --dryrun --skip-null
"""

    argp = ArgumentParserPlus(description=description, epilog=epilog)
    argp.add_argument('--conf', required=True, help="", dest="conf_file")
    argp.add_argument('--overwrite', action="store_true", help="")
    argp.add_argument('--skip-null', action="store_true", help="")
    argp.add_argument('--dryrun', action="store_true", help="")
    argp.add_argument('-v', '--verbose', action='store_true')
    args = argp.parse_args()

    import logging
    if args.verbose:
        log_level = logging.DEBUG
    else:
        log_level = logging.INFO

    simple_stream_logging(log_level)

Esempio n. 6

File: gimsan_result.py Progetto: pnpnpn/gimsan-py

if __name__ == '__main__':
    benchmark = time_benchmark.Benchmark()

    #defaults
    description = """
Generate GIMSAN result
"""

    epilog = """
Examples:

%(prog)s --dir=testout -v
"""

    argp = ArgumentParserPlus(description=description, epilog=epilog)
    argp.add_argument('--dir', required=True, help="main output directory used with gimsan_submit.py")
    argp.add_argument('--overwrite', action="store_true", help="")
    argp.add_argument('--dryrun', action="store_true", help="")
    argp.add_argument('-v', '--verbose', action='store_true')
    args = argp.parse_args()

    import logging
    if args.verbose:
        log_level = logging.DEBUG
    else:
        log_level = logging.INFO

    simple_stream_logging(log_level)
    args.dir = os.path.expanduser(args.dir)