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 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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
biobricks-0.1.64.tar.gz
(13.6 kB
view hashes)
Built Distribution
biobricks-0.1.64-py3-none-any.whl
(11.8 kB
view hashes)
Close
Hashes for biobricks-0.1.64-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 635cfdc74c20ddea32cf68af7e4e590acac55b381e45fdbf7627755c710d2374 |
|
MD5 | 3506b09501aad55e29d21becec54eb1c |
|
BLAKE2b-256 | e908d1cbe44d09042fc7198c7c296f74c6f4ca01e1e090c366325a393179da10 |