Authors | Agustin Maria Pardo |
Github | AgustinPardo |
agustinmpardo@gmail.com |
docker
pythoncyc
PathwayTools installer linux-64 24.0 (https://biocyc.org/download-bundle.shtml)
sudo docker build -t pathway:24.0 .
sudo docker run --name pathwaytools --volume $PWD:/localData --volume $PWD/PGDBs:/opt/data/ptools-local/pgdbs -d -p 5008:5008 pathway:24.0
This comand links the . directory to localData container directory, and create the PGDB folder where the PGDBs reconstructions are stored. Also start a python server that listen on port 5008 to be queried using pythoncyc library (5008 default pythoncyc socket connection).
sudo docker exec pathwaytools bash opt/pathway-tools/pathway-tools -no-patch-download -no-cel-overview -no-web-cel-overview -patho localData/ejemplo
This command create a PGBG itsef, and you should have the genetic-elements.dat, organism-params.dat, and annotation files inside a folder on the . directory. Check the ejemplo folder to see an example of those files or see PathoLogic Batch Mode section 7.6 of the PathwayTools user's manual for more information.
sudo docker container restart pathwaytools
once you successfully run the PGDB reconstrucion you should restart the python server to update the database served.
import pythoncyc
PGDB_list=pythoncyc.all_orgids()
PGDB_list
meta = pythoncyc.select_organism("META")
all_pathways_list=meta.all_pathways(selector='all', base=True)
all_pathways_list
meta = pythoncyc.select_organism("TEST_2")
all_pathways_list=meta.all_pathways(selector='all', base=True)
all_pathways_list
Simple example of PGBDs python queries using pythoncyc library