Metadata-Version: 2.2
Name: CenStats
Version: 0.0.6
Summary: Centromere statistics toolkit.
Author-email: Keith Oshima <oshimak@pennmedicine.upenn.edu>
License: MIT License
Project-URL: Homepage, https://github.com/logsdon-lab/CenStats
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: polars==1.0.0
Requires-Dist: loguru==0.7.2
Requires-Dist: editdistance==0.8.1

# `CenStats`
[![CI](https://github.com/logsdon-lab/centromere-status-checker/actions/workflows/main.yml/badge.svg)](https://github.com/logsdon-lab/centromere-status-checker/actions/workflows/main.yml)
[![PyPI - Version](https://img.shields.io/pypi/v/CenStats)](https://pypi.org/project/CenStats/0.0.1/)

Centromere statistics toolkit.

* `status`
    * Determine the status of centromeric contigs based on [`RepeatMasker`](https://www.repeatmasker.org/) annotations.
* `length`
    * Estimate HOR array length from [`stv`](https://github.com/fedorrik/stv) bed file and [`HumAS-HMMER`](https://github.com/fedorrik/HumAS-HMMER_for_AnVIL) output.
* `nonredundant`
    * Get a non-redundant list of centromeres based on HOR array length from two AS-HOR array length lists. Uses output from `length` command.

### Setup
```bash
pip install censtats
```

### Usage
```bash
usage: censtats [-h] {status,length,nonredundant} ...

Centromere statistics toolkit.

positional arguments:
  {status,length,nonredundant}

options:
  -h, --help       show this help message and exit
```

Read the docs [here](https://github.com/logsdon-lab/CenStats/wiki/Usage).

### Build
```bash
make venv && make build && make install
source venv/bin/activate && censtats -h
```

To run tests:
```bash
source venv/bin/activate && pip install pytest
pytest -s -vv
```
