Metadata-Version: 2.4
Name: tlogo
Version: 0.1.1.dev0
Summary: Sequence logo generator for aligned FASTA files
Author-email: Troy Sincomb <troysincomb@gmail.com>
License: MIT
Keywords: bioinformatics,cli
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: click>=8.0
Requires-Dist: biopython>=1.80
Requires-Dist: matplotlib>=3.5
Requires-Dist: logomaker>=0.8
Requires-Dist: pandas>=1.3
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: hypothesis>=6.0; extra == "dev"
Dynamic: license-file

# tlogo

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

![Window logo example](examples/window_logo.png)

## Install

```bash
pip install tlogo
```

## Development

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

## Usage

```bash
# 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

```bash
pytest -v
```

## Releasing

Version is managed automatically by [setuptools-scm](https://github.com/pypa/setuptools-scm) from git tags:

```bash
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
