ndexbiogridloader 1.0.0

Loads BioGRID data into NDEx

NDEx BioGRID Content Loader

Python application for loading BioGRID data into NDEx.

This tool downloads and unpacks the BioGRID files below

BIOGRID-ORGANISM-4.2.191.tab2.zip

BIOGRID-CHEMICALS-4.2.191.chemtab.zip

NOTE: ndexloadbiogrid.py script --biogridversion parameter dictates version (4.2.191 above)

Dependencies

• ndex2

• ndexutil

• requests

• pandas

• networkx

• scipy

• tqdm

• py4cytoscape

Compatibility

• Python 3.6+

Installation

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

Configuration

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

Usage

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.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

1.0.0 (11-09-2020)

• New default behavior: force-directed-cl layout is now applied on networks via py4cytoscape library and a running instance of Cytoscape. Alternate Cytoscape layouts and the networkx “spring” layout can be run by setting appropriate value via the new –layout flag

0.3.0 (10-27-2020)

• Updated default --biogridversion version to 4.2.191

• All generated networks get networkx spring layout added by default

• Added tqdm progress bar support. Set --noprogressbar flag to disable

• Added –skipupload flag to skip the upload to NDEx step

• Added logic to retry failed upload of network to NDEx. --maxretries and --retry_sleep allow caller to control behavior

• Added --organismfile and --chemicalsfile to let caller override defaults

0.2.0 (2020-07-27)

• Updated default --biogridversion version to 3.5.187

• Modified organism_list file to include 3 strains of coronavirus (SARS-1, SARS-2 and MERS)

• Modified organism_style file to add an orange border to all viral protein nodes. This change affects all the both new and already existing viral organisms.

0.1.3 (2019-11-21)

Fixed a bug where networkType used to be a string, now it is a list of strings and we specify ‘list_of_string’ type when setting networkType attribute with network.set_network_attribute(“networkType”, networkType, ‘list_of_string’). This results in correct representation of networkType in CX model, for example: {“n”:”networkType”,”v”:[“interactome”,”ppi”],”d”:”list_of_string”}.

0.1.2 (2019-10-25)

In organism_load_plan.json, changed types of edge columns “Experimental System Type” and “Throughput” to be “list_of_string”, and “Score” to be “list_of_double”. This change resolves UD-761 Biogrid network can’t be imported to Cytoscape.

0.1.1 (2019-08-23)

• First release on PyPI.