Contributing to Cool-Seq-Tool#

Bug reports and feature requests#

Bugs and new feature requests can be submitted to the Cool-Seq-Tool issue tracker on GitHub. See this StackOverflow post for tips on how to craft a helpful bug report.

Development Setup#

Clone the repository:

git clone https://github.com/genomicmedlab/cool-seq-tool
cd cool-seq-tool

Create a virtual environment and install all dependency groups:

python3 -m venv venv
source venv/bin/activate
python3 -m pip install -e ".[dev,tests,docs]"

We use pre-commit to run conformance tests before commits. This provides checks for:

  • Code format and style

  • Added large files

  • AWS credentials

  • Private keys

Before your first commit, run:

pre-commit install

Style#

Code style is managed by Ruff, and should be checked via pre-commit hook before commits. Final QC is applied with GitHub Actions to every pull request.

Tests#

Tests are executed with pytest:

pytest

Docstring code snippets are also runnable as doctests:

pytest --doctest-modules src/

Documentation#

The documentation is built with Sphinx, which is included in the docs dependency group. Navigate to the docs/ subdirectory and use make to build the HTML version:

# in an existing virtualenv environment
python3 -m pip install -e '.[docs]'
cd docs
make html

See the Sphinx documentation for more information.

transcript_mappings.tsv#

Cool-Seq-Tool uses a static copy of transcript mapping data acquired from Ensembl BioMart. To regenerate this file from the BioMart, select the Human Genes (GRCh38.p13) dataset and choose the following attributes:

  • Gene stable ID

  • Gene stable ID version

  • Transcript stable ID

  • Transcript stable ID version

  • Protein stable ID

  • Protein stable ID version

  • RefSeq match transcript (MANE Select)

  • Gene name

BioMart screenshot

Alternatively, use wags-tails:

>>> from wags_tails import EnsemblTranscriptMappingData
>>> data_fetcher = EnsemblTranscriptMappingData()
>>> data, version = data_fetcher.get_latest()