Biobricks automates bioinformatics data.
Project description
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.
TOKEN
: register at biobricks.ai then go to biobricks.ai/tokenBBLIB
: 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
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