biobricks 0.1.61

Biobricks automates bioinformatics data.

BioBricks

BioBricks makes loading data from biological datasets easy.

pip install biobricks

initialize

To get started configure biobricks with a path for bricks and a biobricks.ai token:

biobricks configure
> Choose path to store bricks: <input a local path>
> Input a token from biobricks.ai/token: <this is your access token>

Pull Bricks

To download a brick and save it locally in your library use bb.pull. An example using the Tox21 dataset:

import biobricks as bb
bb.install('tox21') # save the brick to the brick library and download it's resources
tox21 = bb.load('tox21') # load a SimpleNamespace with all the brick tables

# List the resources in the brick
for tablename in sorted(list(vars(tox21).keys())):
    print(tablename)
    
tox21.tox21_ache_p4.read().to_pandas() # get a pyarrow Table and convert to pandas dataframe

To list the bricks currently available visit github.com/biobricks-ai