README.md

PyGenePlexus

A Python package of the GenePlexus analysis pipeline.

• The ModGenePlexus Method Paper
• The GenePlexusZoo Method Paper
• The GenePlexus Benchmarking Paper
• The Webserver
• The Package Documentation
• Data

Quick start

Installation

Install the GenePlexus package via pip.

pip install geneplexus

Run GenePlexus pipline

Example script

See example/example_run.py for example usage of the API.

For other examples see Package Documentation.

Command-line interface

geneplexus --input_file example/input_genes.txt --output_dir example_result

Run geneplexus --help to see full CLI options.

Dev

Installation

Install the PyGenePlexus package in editable mode with dev dependencies

pip install -e ."[dev]"

Testing

Run the default test suite

pytest test/

By default, test data will be cached. Thus, after the first test run, data redownload will not be tested. To force redownload, specify the --cache-clear option

pytest test/ --cache-clear

Building Documentation

1. Install doc dependencies

pip install -r docs/requirements.txt

2. Build

cd docs
make html

3. Open doc

open build/html/index.html