def test_cooler_info():
filename = op.join('data', 'Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool')
info = hgco.tileset_info(filename)
tiles = hgco.generate_tiles(filename, ['a.0.0.0'])
import base64
r = base64.decodestring(tiles[0][1]['dense'].encode('utf-8'))
q = np.frombuffer(r, dtype=np.float32)
q = q.reshape((256,256))
filename = op.join('data', 'hic-resolutions.cool')
def test_cooler_info():
filename = op.join("data",
"Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool")
hgco.tileset_info(filename)
# TODO: Make assertion about info returned.
tiles = hgco.generate_tiles(filename, ["a.0.0.0"])
r = base64.decodestring(tiles[0][1]["dense"].encode("utf-8"))
q = np.frombuffer(r, dtype=np.float32)
q = q.reshape((256, 256))
filename = op.join("data", "hic-resolutions.cool")
def generate_tiles(tileset_tile_ids):
'''
Generate a tiles for the give tile_ids.
All of the tile_ids must come from the same tileset. This function
will determine the appropriate handler this tile given the tileset's
filetype and datatype
Parameters
----------
tileset: tilesets.models.Tileset object
The tileset that the tile ids should be retrieved from
tile_ids: [str,...]
A list of tile_ids (e.g. xyx.0.0.1) identifying the tiles
to be retrieved
Returns
-------
tile_list: [(tile_id, tile_data),...]
A list of tile_id, tile_data tuples
'''
tileset, tile_ids, raw = tileset_tile_ids
if tileset.filetype == 'hitile':
return generate_hitile_tiles(tileset, tile_ids)
elif tileset.filetype == 'beddb':
return hgbe.tiles(tileset.datafile.path, tile_ids)
elif tileset.filetype == 'bed2ddb' or tileset.filetype == '2dannodb':
return generate_bed2ddb_tiles(tileset, tile_ids)
elif tileset.filetype == 'geodb':
return generate_bed2ddb_tiles(tileset, tile_ids, hggo.get_tiles)
elif tileset.filetype == 'hibed':
return generate_hibed_tiles(tileset, tile_ids)
elif tileset.filetype == 'cooler':
return hgco.generate_tiles(tileset.datafile.path, tile_ids)
elif tileset.filetype == 'bigwig':
chromsizes = get_chromsizes(tileset)
return hgbi.tiles(tileset.datafile.path, tile_ids, chromsizes=chromsizes)
elif tileset.filetype == 'multivec':
return generate_1d_tiles(
tileset.datafile.path,
tile_ids,
ctmu.get_single_tile)
elif tileset.filetype == 'imtiles':
return hgim.get_tiles(tileset.datafile.path, tile_ids, raw)
else:
return [(ti, {'error': 'Unknown tileset filetype: {}'.format(tileset.filetype)}) for ti in tile_ids]
def generate_tiles(tileset_tile_ids):
'''
Generate a tiles for the give tile_ids.
All of the tile_ids must come from the same tileset. This function
will determine the appropriate handler this tile given the tileset's
filetype and datatype
Parameters
----------
tileset_tile_ids: tuple
A four-tuple containing the following parameters.
tileset: tilesets.models.Tileset object
The tileset that the tile ids should be retrieved from
tile_ids: [str,...]
A list of tile_ids (e.g. xyx.0.0.1) identifying the tiles
to be retrieved
raw: str or False
The value of the GET request parameter `raw`.
tileset_options: dict or None
An optional dict containing tileset options, including aggregation options.
Returns
-------
tile_list: [(tile_id, tile_data),...]
A list of tile_id, tile_data tuples
'''
tileset, tile_ids, raw, tileset_options = tileset_tile_ids
if tileset.filetype == 'hitile':
return generate_hitile_tiles(tileset, tile_ids)
elif tileset.filetype == 'beddb':
return hgbe.tiles(tileset.datafile.path, tile_ids)
elif tileset.filetype == 'bed2ddb' or tileset.filetype == '2dannodb':
return generate_bed2ddb_tiles(tileset, tile_ids)
elif tileset.filetype == 'geodb':
return generate_bed2ddb_tiles(tileset, tile_ids, hggo.get_tiles)
elif tileset.filetype == 'hibed':
return generate_hibed_tiles(tileset, tile_ids)
elif tileset.filetype == 'cooler':
return hgco.generate_tiles(tileset.datafile.path, tile_ids)
elif tileset.filetype == 'bigwig':
chromsizes = get_chromsizes(tileset)
return hgbi.tiles(tileset.datafile.path,
tile_ids,
chromsizes=chromsizes)
elif tileset.filetype == 'bigbed':
chromsizes = get_chromsizes(tileset)
return hgbb.tiles(tileset.datafile.path,
tile_ids,
chromsizes=chromsizes)
elif tileset.filetype == 'multivec':
return generate_1d_tiles(tileset.datafile.path, tile_ids,
ctmu.get_single_tile, tileset_options)
elif tileset.filetype == 'imtiles':
return hgim.get_tiles(tileset.datafile.path, tile_ids, raw)
elif tileset.filetype == 'bam':
return ctb.tiles(tileset.datafile.path,
tile_ids,
index_filename=tileset.indexfile.path,
max_tile_width=hss.MAX_BAM_TILE_WIDTH)
else:
filetype = tileset.filetype
filepath = tileset.datafile.path
if filetype in hgti.by_filetype:
return hgti.by_filetype[filetype](filepath).tiles(tile_ids)
return [(ti, {
'error':
'Unknown tileset filetype: {}'.format(tileset.filetype)
}) for ti in tile_ids]