A python library for BIOPAX manipulation
Project description
BIOPAX-Explorer
Features
A python library for BIOPAX manipulation
BIOPAX-Explorer is a Python package, designed to ease the manipulation of BIOPAX datasets. It exploits RDF and SPARQL, using a simple object-oriented, domain specific syntax. Biological Pathway Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. BioPAX is defined in OWL and is represented in the RDF/XML format. using these specifications and formats, BIOPAX-Explorer provides a 100 % compatible object-model with advanced query features, enabling quick analysis of datasets with a low learning curve.
Documentation
The Python code documentation is available on https://fjrmoreews.github.io/biopax-explorer/
Installation
' pip install biopax-explorer '
For large files, use a triple store , do not use the 'direct file in memory' option . the processing time can be long and a lot of RAM is needed.
Prerequisites
The package relies mainly on rdfobj, RDFLib and NetworkX. Optionnaly you can install graph-tool for better performances on large graphs https://graph-tool.skewed.de/static/doc/quickstart.html.
Source repository
Docker installation
ready to use Docker container
We provide a easy to use Docker installation,tested with Docker on Linux and Singularity
The Biopax-Explorer Docker container is available at https://hub.docker.com/r/fjrmore/biopax_explorer
The container can be used to deploy a jupyter enviroment with tutorials and example notebooks
A easy way to test Biopax Explorer is to use docker compose :
# at the root of the repository
docker-compose up
#the triple store (fuseki) will be available on http://localhost:3030/ (login/password admin/admin)
#Jupyter will be available on http://localhost:8888/ (password : pass)
#contain of the docker-compose.yml file:
biopax-explorer:
image: fjrmore/biopax_explorer
volumes:
- ./script/:/work/script
- ./input:/work/input
links:
- "db:tstore"
ports:
- "8888:8888"
command: ["jupyter", "notebook", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root","--NotebookApp.token='pass'" ]
db:
image: stain/jena-fuseki:4.0.0
ports:
- "3030:3030"
volumes:
- ./input/:/staging
- ./db/fuseki:/fuseki
- ./script/:/script
environment:
- JVM_ARGS=-Xmx5024M
- ADMIN_PASSWORD=admin
Linux and Mac installation (Ubuntu and Debian)
pip install biopax-explorer
Windows installation
Installation on windows is possible using at least 2 options :
Installation on Windows using Docker-desktop
This procedure has been tested on Windows 10 Enterprise. first install Docker-desktop : see https://docs.docker.com/docker-for-windows/install/
when Docker-desktop is installed, open a power-shell terminal, then entre the followig commands:
- Biopax-Explorer in Python scripts
$vol= (pwd).Path
docker run -p 81:8888 -p 6006:6006 -it -v ${vol}:/home/user fjrmore/Biopax-Explorer python3 -c "import Biopax-Explorer; print('package p2g OK')"
curl https://gitlab.inria.fr/fmoreews/Biopax-Explorer/-/raw/master/test/test.py -o test.py
docker run -p 81:8888 -p 6006:6006 -it -v ${vol}:/home/user fjrmore/Biopax-Explorer python3 user/test.py
#create your own script (mycript.py) , go in the directory where your script is located and execute it :.
cd script_dir
$vol= (pwd).Path
docker run -p 81:8888 -p 6006:6006 -it -v ${vol}:/home/user fjrmore/Biopax-Explorer python3 mycript.py
How to run power-shell : see this link
- Biopax-Explorer in jupyter lab
$vol= (pwd).Path
docker run -p 81:8888 -p 6006:6006 -it -v ${vol}:/home/user -e SHOW_PWD=true -e JUPYTER_PWD=password fjrmore/Biopax-Explorer jupyter.sh
then launch a browser and go to the following url : http://localhost:81/lab
and enter the password (password)
Installation on Windows using ubuntu terminal
See https://www.microsoft.com/en-us/p/ubuntu-2004-lts/9n6svws3rx71?activetab=pivot:overviewtab
After you're environment configuration, follow the Docker or Conda + pip installation process (see above).
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