Biobricks automates bioinformatics data.
Project description
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 biobrick.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
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