A python client to interact with enviPath
Project description
enviPath Python
Python client for enviPath - the environmental contaminant biotransformation pathway resource.
Quickstart
pip install --upgrade enviPath-python
from pprint import pprint
from enviPath_python import enviPath
eP = enviPath('https://envipath.org')
bbd = eP.get_package('https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1')
bbd_pws = bbd.get_pathways()
pprint(bbd_pws[0].get_description())
Documentation
The enviPath-python documentation can be found here.
If you are new to enviPath our wiki might also contain some value information.
Examples
Searching data
from enviPath_python import enviPath
eP = enviPath('https://envipath.org')
# get package(s) that should be searched
bbd = eP.get_package('https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1')
soil = eP.get_package('https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456')
# returns a dictionary with properly initialized objects
res = eP.search('c1ccccc1', [bbd, soil])
print(res)
# or use a package to search it
res = bbd.search('c1ccccc1')
print(res)
Accessing Data
from pprint import pprint
from enviPath_python import enviPath
eP = enviPath('https://envipath.org')
# get the EAWAG BBD package
bbd = eP.get_package('https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1')
# access collections (e.g. compounds)
# other collections such as reactions, rules, pathways, etc work the same way
compounds = bbd.get_compounds()
for c in compounds[:10]:
print(c.get_id(), c.get_name(), c.get_smiles())
Accessing private data
import getpass
from enviPath_python import enviPath
eP = enviPath('https://envipath.org')
# get username + password
username = input("Enter username")
password = getpass.getpass(prompt="Password for {}".format(username))
eP.login(username, password)
print(eP.who_am_i())
for p in eP.get_packages()[:10]:
print(p)
Predict Pathways
from enviPath_python import enviPath
from enviPath_python.objects import Pathway
from time import sleep
eP = enviPath('https://envipath.org')
# obtain the currently logged in user
me = eP.who_am_i()
# get the package the pathway should be stored in
package = me.get_default_package()
# will trigger the pathway prediction
pw = Pathway.create(package, smiles='CC1(C)C2CCC1(C)C(=O)C2')
# wait until the prediction finished
while pw.is_running():
print("Sleeping for three secs...")
sleep(3)
# check result
if pw.has_failed():
exit(1)
else:
for node in pw.get_nodes():
print(node.get_smiles())
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
enviPath-python-0.2.1.tar.gz
(29.7 kB
view hashes)
Built Distribution
Close
Hashes for enviPath_python-0.2.1-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 2a137cab655d3a6bb238bd60bcd9dbaa6779ff7e572dc5914f8d46baddf870dd |
|
MD5 | e443d3803d275af7a93a203cbce86880 |
|
BLAKE2b-256 | 70bf86e14c70b919b8105d275063a917ae915cd1e8c858fea7ac4fcfc297b5f5 |