Package: ndexbiogridloader
NDEx BioGRID Content LoaderPython application for loading BioGRID data intoNDEx.This tool downloads and unpacks theBioGRIDfiles belowBIOGRID-ORGANISM-4.2.191.tab2.zipBIOGRID-CHEMICALS-4.2.191.chemtab.zipNOTE:ndexloadbiogrid.pyscript--biogridversionparameter dictates version (4.2.191above)Dependenciesndex2ndexutilrequestspandasnetworkxscipytqdmpy4cytoscapeCompatibilityPython 3.6+InstallationFrom PyPi:pip install ndexbiogridloaderBuild from source:git clone https://github.com/ndexcontent/ndexbiogridloader
cd ndexbiogridloader
make dist
pip install dist/ndexloadbiogrid*whlRunmakecommand with no arguments to see other build/deploy options including creation of Docker imagemakeOutput: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 dockerhubConfigurationThendexloadbiogrid.pyrequires a configuration file in the following format be created.
The default path for this configuration is~/.ndexutils.confbut can be overridden with--confflag.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.orgUsageFor information invokendexloadbiogrid.py -hThe command shown below will download the default version of BioGRID files (4.2.191) to the working
directorybiogrid_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_dataNoteBy default Cytoscape must be running to generate the layout for each network. See--layoutflag
options to generate networks without Cytoscape.CreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History1.0.0 (11-09-2020)New default behavior:force-directed-cllayout 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–layoutflag0.3.0 (10-27-2020)Updated default--biogridversionversion to4.2.191All generated networks get networkx spring layout added by defaultAdded tqdm progress bar support. Set--noprogressbarflag to disableAdded –skipupload flag to skip the upload to NDEx stepAdded logic to retry failed upload of network to NDEx.--maxretriesand--retry_sleepallow caller to control
behaviorAdded--organismfileand--chemicalsfileto let caller override
defaults0.2.0 (2020-07-27)Updated default--biogridversionversion to3.5.187Modified 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.