def beddb(filepath, uuid=None, **kwargs): from clodius.tiles.beddb import tileset_info, tiles return Tileset(uuid=uuid, tileset_info=lambda: tileset_info(filepath), tiles=lambda tids: tiles(filepath, tids), **kwargs)
def dfpoints(df, x_col, y_col, uuid=None, **kwargs): """ Generate a tileset that serves 2d labelled points from a pandas dataframe. Parameters ---------- df: :class:`pandas.DataFrame` The dataframe containining the data x_col: str The name of the column containing the x-coordinates y_col: str The name of the column containing the y-coordinates uuid: str The uuid of this tileset Returns ------- A tileset capapble of serving tiles from this dataframe. """ from clodius.tiles.points import tileset_info, tiles, format_data tsinfo = tileset_info(df, x_col, y_col) tiles_fn = lambda z, x, y, width=1, height=1: tiles( df, x_col, y_col, tsinfo, z, x, y, width, height) return Tileset(uuid=uuid, tileset_info=lambda: tsinfo, tiles=lambda tile_ids: format_data( bundled_tiles_wrapper_2d(tile_ids, tiles_fn)), datatype="scatter-point", **kwargs)
def cooler(filepath, uuid=None, **kwargs): from clodius.tiles.cooler import tileset_info, tiles return Tileset(uuid=uuid, tileset_info=lambda: tileset_info(filepath), tiles=lambda tids: tiles(filepath, tids), datatype="matrix", **kwargs)
def bigbed(filepath, uuid=None, chromsizes=None, **kwargs): from clodius.tiles.bigbed import tileset_info, tiles return Tileset( uuid=uuid, tileset_info=lambda: tileset_info(filepath, chromsizes), tiles=lambda tids: tiles(filepath, tids, chromsizes=chromsizes), **kwargs)
def cooler(filepath, uuid=None): return Tileset( tileset_info=lambda: hgco.tileset_info(filepath), tiles=lambda tids: hgco.tiles(filepath, tids), uuid=uuid, track_type="heatmap", track_position="center", )
def bigwig(filepath, uuid=None, chromsizes=None, **kwargs): from clodius.tiles.bigwig import tileset_info, tiles return Tileset( uuid=uuid, tileset_info=lambda: tileset_info(filepath, chromsizes), tiles=lambda tids: tiles(filepath, tids, chromsizes=chromsizes), datatype="vector", **kwargs)
def multivec(filepath, uuid=None, **kwargs): from clodius.tiles.multivec import tileset_info, tiles return Tileset( uuid=uuid, tileset_info=lambda: tileset_info(filepath), tiles=lambda tile_ids: tiles(filepath, tile_ids), **kwargs )
def mrmatrix(filepath, uuid=None, **kwargs): from clodius.tiles.mrmatrix import tileset_info, tiles f = h5py.File(filepath, "r") return Tileset( uuid=uuid, tileset_info=lambda: tileset_info(f), tiles=lambda tile_ids: tiles_wrapper_2d( tile_ids, lambda z, x, y: format_dense_tile(tiles(f, z, x, y))), datatype="matrix", **kwargs)
def tiles(cls, tileset_dict, tids): filetype = tileset_dict.get('filetype', "") if filetype == "bam": data = bam_tiles.tiles( tileset_dict.datafile, tids, index_filename=tileset_dict.index_filename ) elif filetype == "cooler": data = cooler_tiles.tiles(tileset_dict['datafile'], tids) elif filetype == "bigwig": data = bigwig_tiles.tiles(tileset_dict['datafile'], tids) else: data = {'error': f"Unknown tileset filetype: {filetype}"} return data
def test_cooler_tiles(): filename = op.join('data', 'hic-resolutions.cool') hgco.tiles(filename, ['x.0.0.0'])
def test_cooler_tiles(): filename = op.join("data", "hic-resolutions.cool") hgco.tiles(filename, ["x.0.0.0"])