Install

pip install proteoform-regions

Requires Python 3.10–3.12. Core dependencies: pandas, numpy, scipy, biopython, pyteomics, lxml, pyyaml, requests, typer.

Optional extras:

pip install "proteoform-regions[plots]"   # plotting helpers (planned)
pip install "proteoform-regions[dev]"     # pytest, ruff (contributors)
pip install "proteoform-regions[docs]"    # mkdocs-material, mkdocstrings

From source (development)

git clone https://github.com/ShoabSaadat/proteoform-regions
cd proteoform-regions
uv sync --extra dev
uv run pytest -m "not network"

Verify

proteoform-regions --version
proteoform-regions benchmark   # offline ExPASy/UniProt engine check

benchmark compares the package's pI/MW engine against the frozen 16-protein ExPASy reference table packaged with the wheel — it runs fully offline and should print max|d|=0.4200 (the single documented poly-E outlier; all other proteins agree within 0.005 pI).