Rare-GeenuFF (Rare fork of GeenuFF)

The original description of GeenuFF reads:

Schema and API for a relational db that encodes gene models in an explicit, structured, and robust fashion.

This package is a fork of the original GeenuFF, with some quality of life improvements to the code.

Installation

conda env create -f rare-geenuff-conda-env.yml
conda activate rare-geenuff
pip install rare-geenuff

Contents of rare-geenuff-conda-env.yml:

name: rare-geenuff
channels:
  - conda-forge
  - bioconda
dependencies:
  - intervaltree>=3.0.2
  - SQLAlchemy<2,>=1.3.12
  - numpy>=1.18.1
  - pandas
  - biopython
  - pyyaml

beta disclaimer

GeenuFF is currently extremely beta and very unstable. We're keen to get feed back or ideas from the community (even if it's just whether you think this could be useful to you if developed further), but if you build on GeenuFF as it is now, you're doing so at your own risk.

Motivation

We developed this to provide a way of unambiguously encoding gene models, (the way the DNA sequence is interpreted to produce proteins) that is both robust to partial information and biological complexity.

A more extensive description can be found here.

Unit tests

conda install -c conda-forge pytest
git clone -b rare --single-branch https://github.com/anthony-aylward/GeenuFF.git
cd GeenuFF
python -m pytest

usage

You can run the package script command rare-geenuff-example for a quick start with public data:

rare-geenuff-example --download-example-data

This will setup the folder three_algae, download public data in the expected format, and import it into a geenuff spec db for each species. For more information please see the api docs. The --download-example-data option is only necessary the first time running rare-geenuff-example, or if the three_algae folder is not present.

Major plans

• Add a validation module to check structure of gene models.
• Add extraction of raw & mature transcript, CDS, and protein sequence as a demo application.
• Visualization.

Thanks

To @janinamass for discussion and advice.