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