Python application for loading BioGRID data into NDEx.
This tool downloads and unpacks the BioGRID files below
NOTE: ndexloadbiogrid.py script --biogridversion parameter dictates version (4.2.191 above)
- Python 3.6+
From PyPi:
pip install ndexbiogridloader
Build from source:
git clone https://github.com/ndexcontent/ndexbiogridloader cd ndexbiogridloader make dist pip install dist/ndexloadbiogrid*whl
Run make command with no arguments to see other build/deploy options including creation of Docker image
make
Output:
clean remove all build, test, coverage and Python artifacts clean-build remove build artifacts clean-pyc remove Python file artifacts clean-test remove test and coverage artifacts lint check style with flake8 test run tests quickly with the default Python test-all run tests on every Python version with tox coverage check code coverage quickly with the default Python docs generate Sphinx HTML documentation, including API docs servedocs compile the docs watching for changes testrelease package and upload a TEST release release package and upload a release dist builds source and wheel package install install the package to the active Python's site-packages dockerbuild build docker image and store in local repository dockerpush push image to dockerhub
The ndexloadbiogrid.py requires a configuration file in the following format be created.
The default path for this configuration is ~/.ndexutils.conf but can be overridden with
--conf flag.
Format of configuration file:
[<value in --profile (default ndexbiogridloader)>] user = <NDEx username> password = <NDEx password> server = <NDEx server(omit http) ie public.ndexbio.org>
Example of default configuration file:
[ndexbiogridloader] user = joe123 password = somepassword123 server = dev.ndexbio.org
For information invoke ndexloadbiogrid.py -h
The command shown below will download the default version of BioGRID files (4.2.191) to the working
directory biogrid_data, will generate CX networks in this directory, and then upload these networks
to default account specified in [ndexbiogridloader] section of default configuration file:
ndexloadbiogrid.py biogrid_data
Note
By default Cytoscape must be running to generate the layout for each network. See --layout flag
options to generate networks without Cytoscape.
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.