コード例 #1
0
ファイル: modifications.py プロジェクト: lpp1985/lpp_Script 
def add_options_to_parser(p):
    from pbreports.io.validators import validate_file
    p.description = __doc__  # FIXME which is probably wrong
    p.version = __version__
    p = add_base_and_plot_options(p)
    p.add_argument("basemods_h5", help="modifications.h5", type=validate_file)
    p.set_defaults(func=_args_runner)
    return p
コード例 #2
0
ファイル: modifications.py プロジェクト: natechols/pbreports 
def add_options_to_parser(p):
    from pbreports.io.validators import validate_file
    p.description = __doc__  # FIXME which is probably wrong
    p.version = __version__
    p = add_base_and_plot_options(p)
    p.add_argument("basemods_h5", help="modifications.h5", type=validate_file)
    p.set_defaults(func=_args_runner)
    return p
コード例 #3
0
ファイル: control.py プロジェクト: skinner/pbreports 
def add_options_to_parser(p):
    desc = 'Generates a report showing control quality and readlength information.'
    p.description = desc
    p.version = __version__
    p = add_base_and_plot_options(p)
    p.add_argument("cntrCmpH5", help="control_reads.cmp.h5", type=validate_file)
    p.add_argument("csv", help="filtered_summary.csv", type=validate_file)

    p.set_defaults(func=args_runner)
    return p
コード例 #4
0
def add_options_to_parser(p):
    desc = spec.description
    p.description = desc
    p.version = __version__
    p = add_base_and_plot_options(p)
    p.add_argument("cntrCmpH5", help="control_reads.cmp.h5",
                   type=validate_file)
    p.add_argument("csv", help="filtered_summary.csv", type=validate_file)

    p.set_defaults(func=args_runner)
    return p
コード例 #5
0
def add_options_to_parser(p):
    desc = 'Generates a report showing control quality and readlength information.'
    p.description = desc
    p.version = __version__
    p = add_base_and_plot_options(p)
    p.add_argument("cntrCmpH5",
                   help="control_reads.cmp.h5",
                   type=validate_file)
    p.add_argument("csv", help="filtered_summary.csv", type=validate_file)

    p.set_defaults(func=args_runner)
    return p
コード例 #6
0
ファイル: coverage.py プロジェクト: skinner/pbreports 
def add_options_to_parser(p):
    desc = 'Generates a report showing coverage plots for the top 25 contigs of the supplied reference.'
    p.description = desc
    p.version = __version__
    p = add_base_and_plot_options(p)
    p.add_argument("reference", help="reference file or directory", type=str)
    p.add_argument("gff", help="alignment_summary.gff", type=validate_file)
    p.add_argument("--maxContigs", action="store", default=25,
                   help="Max number of contigs to plot. Defaults to 25.")

    p.set_defaults(func=args_runner)
    return p
コード例 #7
0
def add_options_to_parser(p):
    desc = spec.description
    p.description = desc
    p.version = __version__
    p = add_base_and_plot_options(p)
    p.add_argument("cntrCmpH5",
                   help="control_reads.cmp.h5",
                   type=validate_file)
    p.add_argument("csv", help="filtered_summary.csv", type=validate_file)

    p.set_defaults(func=args_runner)
    return p