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

To help you get started, we’ve selected a few bioframe examples, based on popular ways it is used in public projects.

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github mirnylab / bioframe / bioframe / resources.py View on Github external
def fetch_ucsc_centromeres(db,**kwargs):
    return read_table(
        'http://hgdownload.cse.ucsc.edu/goldenPath/{}/database/centromeres.txt.gz'.format(db),
        schema='centromeres',
        **kwargs)
github mirnylab / bioframe / bioframe / resources.py View on Github external
def fetch_ucsc_cytoband(db, ideo=True, **kwargs):
    if ideo:
        return read_table(
            'http://hgdownload.cse.ucsc.edu/goldenPath/{}/database/cytoBandIdeo.txt.gz'.format(db),
            schema='cytoband',
            **kwargs)
    else:
        return read_table(
            'http://hgdownload.cse.ucsc.edu/goldenPath/{}/database/cytoBand.txt.gz'.format(db),
            schema='cytoband',
            **kwargs)
github mirnylab / bioframe / bioframe / resources.py View on Github external
    path[:-12]: lambda : read_table(
        pkg_resources.resource_filename(__name__, 'data/'+path),
        SCHEMAS['bed3'])
    for path in pkg_resources.resource_listdir(__name__, 'data/')