How to use the pygtftk.arg_formatter.ranged_num function in pygtftk

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github dputhier / pygtftk / pygtftk / plugins / closest_gn_to_feat.py View on Github external
parser_grp.add_argument('-t', '--ft-type',
                            help="The feature of interest.",
                            default='gene',
                            choices=['gene', 'transcript', 'tss', 'tts'],
                            required=False)

    parser_grp.add_argument('-n', '--names',
                            help="The key(s) that should be used as name in the output BED file.",
                            default="gene_id,gene_name",
                            metavar="NAME",
                            type=str)

    parser_grp.add_argument('-p', '--slop-value',
                            help="Look until this number of nucleotides in 5' and 3' direction",
                            default=0,
                            type=arg_formatter.ranged_num(lowest=0, highest=None,
                                                          val_type="int", linc=True),
                            required=False)

    parser_grp.add_argument('-u', '--uncollapse',
                            help='Write one peak to gene/distance per line (no comma separated list).',
                            action="store_true")

    parser_grp.add_argument('-g', '--gene-centric',
                            help='Print --feature-type coordinate and the peak list and associated distance.',
                            action="store_true")

    parser_grp.add_argument('-c', '--chrom-info',
                            help='Tabulated file (chr as column 1, sizes as column 2.)',
                            default=None,
                            action=CheckChromFile,
                            required=True)
github dputhier / pygtftk / pygtftk / plugins / mk_matrix.py View on Github external
parser_grp.add_argument('-t', '--ft-type',
                            help='If input is a GTF, the region to analyse.',
                            default='promoter',
                            choices=['promoter',
                                     'tts',
                                     'transcript',
                                     'user_regions',
                                     'single_nuc'],
                            type=str,
                            required=False)

    parser_grp.add_argument('-p', '--pseudo-count',
                            help='Pseudo-count to add to all values.',
                            default=0,
                            type=arg_formatter.ranged_num(lowest=0, highest=None,
                                                          val_type="float", linc=True),
                            required=False)

    parser_grp.add_argument('-u', '--upstream',
                            help="Extend the region of interest in 5' by a given value.",
                            default=1000,
                            type=arg_formatter.ranged_num(lowest=0, highest=None,
                                                          val_type="int", linc=True),
                            required=False)

    parser_grp.add_argument('-d', '--downstream',
                            help="Extend the region of interest in 3' by a given value.",
                            default=1000,
                            type=arg_formatter.ranged_num(lowest=0, highest=None,
                                                          val_type="int", linc=True),
                            required=False)
github dputhier / pygtftk / pygtftk / plugins / ologram.py View on Github external
parser_grp.add_argument('-m', '--more-keys',
                            help='A comma separated list of key used for labeling the genome. See Notes.',
                            type=str,
                            default=None,
                            required=False)

    parser_grp.add_argument('-n', '--no-basic-feature',
                            help="No statistics for basic features of GTF. Concentrates on --more-bed and --more-keys.",
                            action="store_true",
                            required=False)

    # --------------------- Backend ------------------------------------------ #

    parser_grp.add_argument('-k', '--nb-threads',
                            help='Number of threads for multiprocessing.',
                            type=arg_formatter.ranged_num(0, None),
                            default=1,
                            required=False)

    parser_grp.add_argument('-s', '--seed',
                            help='Numpy random seed.',
                            type=arg_formatter.ranged_num(None, None),
                            default=42,
                            required=False)

    parser_grp.add_argument('-mn', '--minibatch-nb',
                            help='Number of minibatches of shuffles.',
                            type=arg_formatter.ranged_num(0, None),
                            default=10,
                            required=False)

    parser_grp.add_argument('-ms', '--minibatch-size',
github dputhier / pygtftk / pygtftk / plugins / random_list.py View on Github external
help="Path to the GTF file. Default to STDIN",
                            default=sys.stdin,
                            metavar="GTF",
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="GTF",
                            type=arg_formatter.FormattedFile(mode='w', file_ext=('gtf')))

    parser_grp.add_argument('-n', '--number',
                            help="The number of transcripts or gene to select.",
                            default=1,
                            metavar="NUMBER",
                            type=arg_formatter.ranged_num(lowest=1,
                                                          highest=None,
                                                          linc=True,
                                                          val_type='int'),
                            required=False)

    parser_grp.add_argument('-t', '--ft-type',
                            help="The type of feature.",
                            default="transcript",
                            choices=["gene", "transcript"],
                            required=False)

    parser_grp.add_argument('-s', '--seed-value',
                            help="Seed value for the random number generator.",
                            default=None,
                            metavar="SEED",
                            type=arg_formatter.ranged_num(lowest=1,
github dputhier / pygtftk / pygtftk / plugins / random_tx.py View on Github external
parser_grp.add_argument('-m', '--max-transcript',
                            help="The maximum number of transcripts to select for each gene.",
                            default=1,
                            metavar="MAX",
                            type=arg_formatter.ranged_num(lowest=1,
                                                          highest=None,
                                                          linc=True,
                                                          val_type='int'),
                            required=False)

    parser_grp.add_argument('-s', '--seed-value',
                            help="Seed value for the random number generator.",
                            default=None,
                            metavar="SEED",
                            type=arg_formatter.ranged_num(lowest=1,
                                                          highest=None,
                                                          linc=True,
                                                          val_type='int'),
                            required=False)

    return parser
github dputhier / pygtftk / pygtftk / plugins / select_by_key.py View on Github external
help='A comma-separated list of values.',
                            default=None,
                            metavar="VALUE",
                            type=str)

    parser_mut.add_argument('-f', '--file-with-values',
                            help='A file containing values as a single column.',
                            default=None,
                            metavar="FILE",
                            type=argparse.FileType("r"))

    parser_grp.add_argument('-c', '--col',
                            help='The column number (one-based) that contains the values in the file. File is tab-delimited.',
                            default=1,
                            metavar="COL",
                            type=arg_formatter.ranged_num(lowest=1,
                                                          highest=None,
                                                          linc=True,
                                                          val_type='int'),
                            required=False)

    parser_grp.add_argument('-n', '--invert-match',
                            help='Not/invert match. Select lines whose selected key is not associated'
                                 ' with the selected values.',
                            action="store_true")

    parser_grp.add_argument('-b', '--bed-format',
                            help='Ask for bed format output.',
                            action="store_true")

    parser_grp.add_argument('-m', '--names',
                            help="If Bed output. The key(s) that should be used as name.",
github dputhier / pygtftk / pygtftk / plugins / merge_ologram_stats.py View on Github external
def make_parser():
    """The main argument parser."""
    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('inputfiles',
                            help="Complete paths to the OLOGRAM output files",
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('txt')),
                            nargs='+')

    parser_grp.add_argument('-pw', '--pdf-width',
                            help='Output pdf file width (inches).',
                            type=arg_formatter.ranged_num(0, None),
                            default=None,
                            required=False)

    parser_grp.add_argument('-ph', '--pdf-height',
                            help='Output pdf file height (inches).',
                            type=arg_formatter.ranged_num(0, None),
                            default=None,
                            required=False)

    parser_grp.add_argument('-o', '--output',
                            help="Pdf file name.",
                            default=None,
                            nargs=None,
                            type=arg_formatter.FormattedFile(mode='w', file_ext='pdf'),
                            required=True)