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tlogo

Sequence logo generator for aligned FASTA files with HxB2 coordinate mapping for HIV Env.

Window logo example

Install

pip install tlogo

Development

git clone https://github.com/tmsincomb/tlogo.git
cd tlogo
pip install -e ".[dev]"

Usage

# Standard logo at specific HxB2 positions
tlogo logo alignment.fasta --positions 130,160,332

# Logo for an entire Env region
tlogo logo alignment.fasta --region V3

# Per-animal window logo around a single position
tlogo window alignment.fasta --position 100 --radius 7

# Auto-detect variant positions and generate window logos
tlogo auto alignment.fasta --variant-freq 0.5

Testing

pytest -v

Releasing

Version is managed automatically by setuptools-scm from git tags:

git tag v0.1.0
git push origin v0.1.0

PyPI publishing is handled by GitHub Actions via trusted publishing (OIDC). Configure your PyPI project to trust the publish.yml workflow.

License

MIT