biobricks 0.1.39

Biobricks automates bioinformatics data.

BioBricks

BioBricks makes loading data from biological datasets easy.

pip install biobricks

initialize

To initialize BioBricks you must set the BBLIB environmental variable and get a user token.

1. TOKEN: register at biobricks.ai then go to biobricks.ai/token
2. BBLIB: Set this to a path on your local file system with plenty of space for large bricks

import biobricks as bb
os.environ['BBLIB'] = '/some/path' # typically set this up to persist between python sessions
bb.initialize(<TOKEN>) # see step 1 above

Pull Bricks

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

bb.pull('tox21') # save the brick to BBLIB 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.to_pandas() # get a pyarrow Table and convert to pandas dataframe

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