Metadata-Version: 2.4
Name: intronator
Version: 0.2.0
Summary: A Python package for comprehensive splice site analysis and simulation
Home-page: https://github.com/intronator/intronator
Author: Intronator Team
Author-email: Intronator Team <contact@intronator.org>
Maintainer-email: Intronator Team <contact@intronator.org>
License-Expression: MIT
Project-URL: Homepage, https://github.com/intronator/intronator
Project-URL: Documentation, https://intronator.readthedocs.io
Project-URL: Repository, https://github.com/intronator/intronator
Project-URL: Bug Tracker, https://github.com/intronator/intronator/issues
Keywords: bioinformatics,splicing,genomics,splice-sites,RNA,mutations
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: seqmat
Requires-Dist: numpy>=1.21.0
Requires-Dist: pandas>=1.3.0
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: black; extra == "dev"
Requires-Dist: isort; extra == "dev"
Requires-Dist: flake8; extra == "dev"
Provides-Extra: ml
Requires-Dist: torch>=1.10.0; extra == "ml"
Requires-Dist: tensorflow>=2.8.0; extra == "ml"
Requires-Dist: keras>=2.8.0; extra == "ml"
Requires-Dist: absl-py; extra == "ml"
Provides-Extra: external
Requires-Dist: spliceai; extra == "external"
Dynamic: author
Dynamic: home-page
Dynamic: license-file
Dynamic: requires-python

# Intronator

A Python package for intron analysis with splice site prediction capabilities.

## Features

- SpliceAI integration for splice site prediction
- Pangolin model support for enhanced predictions
- seqmat compatibility for sequence analysis
- Python 3.10+ support

## Installation

### Basic Installation
```bash
pip install intronator
```

### External Dependencies
The package requires SpliceAI and Pangolin models which must be installed separately:

#### SpliceAI
```bash
pip install spliceai
```

#### Pangolin
```bash
pip install git+https://github.com/tkzeng/Pangolin.git
```

#### Complete Installation (with external dependencies)
```bash
pip install intronator[external]
```

## Quick Start

```python
import intronator

# Check package status
print(intronator.hello_intronator())
print(intronator.check_seqmat_compatibility())
print(intronator.get_model_status())
```

## Requirements

- Python >= 3.10
- seqmat
- torch >= 1.10.0
- tensorflow >= 2.8.0
- SpliceAI (install separately)
- Pangolin (install separately)

## Notes

- SpliceAI and Pangolin models will be automatically loaded when the package is imported
- Model loading may take some time on first import
- GPU acceleration is automatically detected and used when available
