Metadata-Version: 2.4
Name: methurator
Version: 2.2.0
Summary: Python package designed to estimate CpGs saturation for DNA methylation sequencing data.
Author-email: Edoardo Giuili <edoardogiuili@gmail.com>
License: MIT License
        
        Copyright (c) 2025 Edoardo Giuili, TOBI lab
        
        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
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Project-URL: Changelog, https://github.com/VIBTOBIlab/methurator/blob/main/CHANGELOG.md
Project-URL: Documentation, https://github.com/VIBTOBIlab/methurator/README.md
Project-URL: Issues, https://github.com/VIBTOBIlab/methurator/issues
Project-URL: Repository, https://github.com/VIBTOBIlab/methurator
Keywords: bioinformatics,biology,BSseq,methylation,RRBS
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: <3.14,>=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: packaging>=24
Requires-Dist: pandas
Requires-Dist: pyfaidx
Requires-Dist: pysam
Requires-Dist: pyyaml
Requires-Dist: rich
Requires-Dist: rich-click
Requires-Dist: scipy
Requires-Dist: tqdm
Requires-Dist: plotly
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-xdist; extra == "dev"
Dynamic: license-file

# 🧬 methurator

[![Python](https://img.shields.io/badge/python-≥3.10%20&%20≤3.13-blue.svg)](https://www.python.org/)
[![License](https://img.shields.io/badge/License-MIT-green.svg)](LICENSE)
[![pytest](https://img.shields.io/badge/tested%20with-pytest-blue.svg)](https://pytest.org/)
[![BioConda](https://img.shields.io/badge/bioconda-methurator-brightgreen.svg?logo=anaconda)](https://anaconda.org/bioconda/methurator)
[![BioContainer](https://img.shields.io/badge/biocontainer-methurator-0A7BBB.svg?logo=docker)](https://quay.io/repository/biocontainers/methurator)

---

## 🚀 What is methurator?

> **Note**: For detailed documentation, command reference, and advanced usage, see the [docs here](https://vibtobilab.github.io/methurator/latest/).

**methurator** is a Python package to estimate CpG sequencing saturation for DNA methylation sequencing data.

---

## ✨ Key features

- Extrapolate CpG discovery beyond observed sequencing depth
- Compute theoretical asymptotes
- Optional bootstrap confidence intervals
- Interactive HTML plots
- BioConda and BioContainer support

## 📦 Installation

### pip

```bash
pip install methurator
```

### BioConda (recommended)

```bash
conda create -n methurator_env methurator
conda activate methurator_env
```

### Container

```bash
docker pull quay.io/biocontainers/methurator
```

## Example Workflow

```bash
# Run Chao estimator on BAM file
methurator gt-estimator --genome hg19 my_sample.bam --compute_ci

# Generate plots from the results
methurator plot --summary output/methurator_summary.yml
```
