How to use the bioframe.formats.read_chromsizes function in bioframe

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github mirnylab / bioframe / bioframe / resources.py View on Github external
"""
    Download chromosome sizes from UCSC as a :class:`pandas.Series`, indexed
    by chromosome label.

    Parameters
    ----------
    db : str
        The name of a UCSC genome assembly.

    Other Parameters
    ----------------
    **kwargs :
        Passed to :func:`read_chromsizes`.

    """
    return read_chromsizes(
        'http://hgdownload.cse.ucsc.edu/goldenPath/{}/database/chromInfo.txt.gz'.format(db),
        **kwargs)
github mirnylab / bioframe / bioframe / resources.py View on Github external
    path[:-12]: lambda : read_chromsizes(
        pkg_resources.resource_filename(__name__, 'data/'+path))
    for path in pkg_resources.resource_listdir(__name__, 'data/')