Python add_io_args示例

示例#1

def get_argument_parser():

    desc = 'Extract GO-PCA signatures as a tab-delimited text file.'
    parser = arguments.get_argument_parser(desc=desc)
    arguments.add_io_args(parser)

    return parser

示例#2

文件： extract_signature_matrix.py 项目： JohnWSteill/gopca

def get_argument_parser():

    desc = 'Extract the GO-PCA signatures matrix as a tab-delimited text file.'
    parser = arguments.get_argument_parser(desc=desc)

    arguments.add_io_args(parser)
    arguments.add_signature_args(parser)
    arguments.add_sample_args(parser)
    arguments.add_reporting_args(parser)

    return parser

示例#3

文件： convert_to_matlab.py 项目： flo-compbio/gopca

def get_argument_parser():

    desc = 'Converts GO-PCA result to MATLAB format.'
    parser = arguments.get_argument_parser(desc=desc)

    arguments.add_io_args(parser)
    # arguments.add_reporting_args(parser)

    parser.add_argument('--append-mat', action='store_true',
                        help='Automatically append .mat file extension.')

    return parser

示例#4

def get_argument_parser():

    desc = 'Converts GO-PCA result to MATLAB format.'
    parser = arguments.get_argument_parser(desc=desc)

    arguments.add_io_args(parser)
    # arguments.add_reporting_args(parser)

    parser.add_argument('--append-mat',
                        action='store_true',
                        help='Automatically append .mat file extension.')

    return parser

示例#5

文件： plot_signature_matrix.py 项目： milescsmith/gopca

def get_argument_parser():
    desc = 'Generate an interactive plot of the GO-PCA signature matrix.'
    parser = arguments.get_argument_parser(desc=desc)
    arguments.add_io_args(parser)
    arguments.add_reporting_args(parser)
    # arguments.add_sample_args(parser)
    arguments.add_figure_args(parser)
    arguments.add_heatmap_args(parser)

    g = parser.add_argument_group('Plotting options')
    g.add_argument(
        '--no-plotly-js', action='store_true',
        help='Do not include plotly javascript code in figure.')
    
    return parser

示例#6

文件： filter_signatures.py 项目： flo-compbio/gopca

def get_argument_parser():

    desc = 'Filter redundant GO-PCA signatures.'
    parser = arguments.get_argument_parser(desc=desc)

    g = parser.add_argument_group('Filtering options')

    arguments.add_io_args(parser)
    float_mv = arguments.float_mv

    g.add_argument(
        '-r', '--corr-thresh', type=float, required=True, metavar=float_mv,
        help=textwrap.dedent("""\
            Correlation threshold for filtering signatures
            (1.0 = off)."""))

    arguments.add_reporting_args(parser)

    return parser

示例#7

文件： filter_signatures.py 项目： milescsmith/gopca

def get_argument_parser():

    desc = 'Filter redundant GO-PCA signatures.'
    parser = arguments.get_argument_parser(desc=desc)

    g = parser.add_argument_group('Filtering options')

    arguments.add_io_args(parser)
    float_mv = arguments.float_mv

    g.add_argument('-r',
                   '--corr-thresh',
                   type=float,
                   required=True,
                   metavar=float_mv,
                   help=textwrap.dedent("""\
            Correlation threshold for filtering signatures
            (1.0 = off)."""))

    arguments.add_reporting_args(parser)

    return parser

示例#8

def get_argument_parser():
    desc = 'Extract GO-PCA signatures as an Excel spreadsheet.'
    parser = arguments.get_argument_parser(desc=desc)
    arguments.add_io_args(parser)
    return parser

示例#9

文件： extract_signatures.py 项目： flo-compbio/gopca

def get_argument_parser():
    desc = 'Extract GO-PCA signatures as a tab-delimited text file.'
    parser = arguments.get_argument_parser(desc=desc)
    arguments.add_io_args(parser)
    arguments.add_reporting_args(parser)
    return parser

示例#10

文件： extract_signatures_excel.py 项目： flo-compbio/gopca

def get_argument_parser():
    desc = 'Extract GO-PCA signatures as an Excel spreadsheet.'
    parser = arguments.get_argument_parser(desc=desc)
    arguments.add_io_args(parser)
    arguments.add_reporting_args(parser)
    return parser