NDEx NeST SubNetworks Content Loader

Extracts Nested Systems in Tumors NeST subnetworks from NeST Map - Main Model and loads them as new networks in NDEx

Loads NDEx NeST SubNetworks Content Loader data into NDEx (http://ndexbio.org). This is done by doing the following:

1. Load the NeST Map - Main Model as specified by --nest https://www.ndexbio.org/viewer/networks/9a8f5326-aa6e-11ea-aaef-0ac135e8bacf
2. Load IAS_score.tsv file from url or path specified by --ias_score
3. Find all named, assemblies (nodes) that have Annotation with a name that does not start with NEST: and have --maxsize genes or less in Gene attribute
4. For each named assembly create subnetwork by extracting edges from IAS_score.tsv file that pertain to proteins in Genes attribute and use the name in Annotation attribute for network name
5. Apply a default style to network, as well as set description, version, reference, Prov:generatedBy, Prov:derivedFrom fields

• Free software: MIT license
• Documentation: https://ndexnestloader.readthedocs.io.

Dependencies

• ndex2
• ndexutil

Compatibility

• Python 3.8+

Installation

git clone https://github.com/ndexcontent/ndexnestloader
cd ndexnestloader
make dist
pip install dist/ndexloadnestsubnetworks*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 ndexloadnestsubnetworks.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 ndexnestloader)>]

user = <NDEx username>
password = <NDEx password>
server = <NDEx server(omit http) ie public.ndexbio.org>

Example configuration file

[ndexnestloader_dev]

user = joe123
password = somepassword123
server = dev.ndexbio.org

Needed files

TODO: Add description of needed files

Usage

For information invoke ndexloadnestsubnetworks.py -h

Example usage

TODO: Add information about example usage

ndexloadnestsubnetworks.py # TODO Add other needed arguments here

Via Docker

Example usage

TODO: Add information about example usage

Coming soon...

Credits

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