Metadata-Version: 2.4
Name: exonize
Version: 1.1.2
Summary: A tool for finding duplicated exons in annotated genomes
Author: Marina Herrera Sarrias, Christopher Wheat, Liam Longo, Lars Arvestad
Maintainer-email: Lars Arvestad <arve@math.su.se>
License: MIT License
        
        Copyright (c) 2024 Marina Sarrias
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: gffutils
Requires-Dist: portion
Requires-Dist: biopython
Requires-Dist: networkx
Requires-Dist: matplotlib
Requires-Dist: pandas
Dynamic: license-file

```
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██╔══╝   ██╔██╗ ██║   ██║██║╚██╗██║██║ ███╔╝  ██╔══╝
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╚══════╝╚═╝  ╚═╝ ╚═════╝ ╚═╝  ╚═══╝╚═╝╚══════╝╚══════╝
Marina Herrera Sarrias, Department of Mathematics, Stockholm University
Christopher Wheat, Department of Zoology, Stockholm University
Liam M. Longo, Earth-Life Science Institute (ELSI), Institute of Science Tokyo
Lars Arvestad, Department of Mathematics, Stockholm University
```

[![PyPI version](https://badge.fury.io/py/exonize.svg)](https://badge.fury.io/py/exonize)
[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=msarrias_exonize&metric=alert_status)](https://sonarcloud.io/dashboard?id=msarrias_exonize)

## Welcome!
`exonize` is an open-source command-line tool and [Python package](https://pypi.org/project/exonize/) for identifying and classifying coding exon duplications in annotated genomes. `exonize` identifies full exon duplications using local and global alignment methods and implements a graph-based framework to handle clusters of exons formed by repetitive duplication events. `exonize` introduces a classification schema to categorize the interdependence between duplicated exons (or groups of exons) across transcripts. For data parsing and downstream analysis, we introduce `exonize_analysis` a Python module within the `exonize` package.

## Documentation

Please see the [Documentation](https://msarrias.github.io/exonize/) for a full user guide and an introductory tutorial to the `exonize_analysis` module.

## Installation

You are best off installing `exonize` from [PyPI.org](https://pypi.org/project/Exonize/1.0/) using

```bash
pip install exonize
```

If installing from the [GitHub](https://github.com/msarrias/exonize) repo

```bash
git clone git@github.com:msarrias/exonize.git
cd exonize
pip install .
```

You should now be able to run `exonize -h`.

`exonize` is tested with Python 3.9, 3.10, 3.11, 3.12

## Requirements

`exonize` requires a local installation of:


* [`BLAST+`](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html) \[[download link](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)\]  
* [`MUSCLE (v.5.3)`](https://www.drive5.com/muscle/) \[[download link](https://github.com/rcedgar/muscle/releases)\]  
* [`SQLite`](https://www.sqlite.org/index.html)[[download link](https://www.sqlite.org/download.html)]



## Support

If you need help with `exonize`, contact us! To report a bug or request a new feature, open an **[Issue](https://github.com/msarrias/exonize/issues)** on the `exonize` repo.

## Citation

If you use `exonize` in a publication, please cite:
```
TBA
```

