Metadata-Version: 2.1
Name: flucleave
Version: 0.1.2
Summary: Deep learning prediction of influenza virus pathogenicity from HA cleavage sites
Author-email: Cameron Norris <cameron.norris@usda.gov>
License: MIT
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: tensorflow>=2.8.0
Requires-Dist: pandas>=1.4.0
Requires-Dist: numpy>=1.21.0
Requires-Dist: biopython>=1.79
Requires-Dist: scikit-learn>=1.0.0
Requires-Dist: click>=8.0.0
Provides-Extra: dev
Requires-Dist: pytest>=7.0.0; extra == "dev"
Requires-Dist: black>=22.0.0; extra == "dev"
Requires-Dist: ruff>=0.1.0; extra == "dev"
Requires-Dist: mypy>=1.0.0; extra == "dev"

# FluCleave

Deep learning prediction of influenza virus pathogenicity from HA cleavage sites.

## Features

-   Analyzes hemagglutinin (HA) cleavage site sequences
-   Predicts high/low pathogenicity using deep learning
-   Handles both DNA and protein sequences
-   Command-line interface for easy use
-   Trained on curated dataset of known pathogenic sequences

## Installation

```bash
pip install flucleave
```

## Usage

Predict pathogenicity from FASTA file:

```bash
flucleave predict --fasta sequences.fasta --output-dir results/ --prefix sample_name
```

Train new model (optional):

```bash
flucleave train --training-csv data.csv
```

## Data Format

Input FASTA should contain HA protein sequences in either amino acid or DNA format.

## License

FluCleave is licensed under the [MIT License](LICENSE).
