cellmaps-ppidownloader 0.2.0

A tool to download AP-MS data for Cell Maps pipeline

Cell Maps for AI PPI Downloader

The Cell Maps PPI Downloader is part of the Cell Mapping Toolkit

Downloads protein-protein interaction data

• Free software: MIT license

• Documentation: https://cellmaps-ppidownloader.readthedocs.io.

Dependencies

• cellmaps_utils

• requests

• mygene

• tqdm

Compatibility

• Python 3.8+

Installation

git clone https://github.com/idekerlab/cellmaps_ppidownloader
cd cellmaps_ppidownloader
make dist
pip install dist/cellmaps_ppidownloader*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

Before running tests, please install pip install -r requirements_dev.

Needed files

• bait list file: TSV file of baits used for AP-MS experiments

• edge list file: TSV file of edges for protein interaction network

• provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)

Usage

For information invoke cellmaps_ppidownloadercmd.py -h

Example usage

cellmaps_ppidownloadercmd.py ./cellmaps_ppidownloader_outdir --edgelist examples/edgelist.tsv --baitlist examples/baitlist.tsv --provenance examples/provenance.json

Via Docker

Example usage

Coming soon...

Credits

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

History

0.2.0 (2024-12-02)

• Added README generation.

• Refactor code.

0.1.2 (2024-09-12)

• Bug fix in adding gene node attributes.

0.1.1 (2024-08-26)

• Bug fix in adding gene node attributes. The bug was resulting in duplicate entries and missing gene names, related to ambiguous antibodies.

0.1.0 (2024-01-01)

• First release on PyPI.