Metadata-Version: 2.4
Name: simulate_damage
Version: 0.1.4
Summary: Simulate ancient DNA deamination damage on paired-end FASTQ files
Home-page: https://github.com/yourusername/simulate_damage
Author: Andrew Tedder
Author-email: Andrew Tedder <a.tedder@bradford.ac.uk>
License: MIT
Project-URL: Homepage, https://github.com/atedder/simulate_damage
Project-URL: Source, https://github.com/atedder/simulate_damage
Project-URL: Tracker, https://github.com/atedder/simulate_damage/issues
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: biopython
Dynamic: author
Dynamic: home-page
Dynamic: requires-python

# simulate_damage

`simulate_damage` is a command-line tool that simulates ancient DNA (aDNA) deamination damage in **paired-end FASTQ** files. It introduces realistic C→T and G→A transitions at read ends and internally, allowing researchers to test pipelines under damage conditions typical of ancient samples.

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##  Features

-  Supports **.fastq** and **.fastq.gz**
-  Handles **paired-end reads** automatically
-  Allows **custom damage rates** for 5′ and internal C→T (R1) and G→A (R2)
-  Keeps **original read qualities** and structure
-  Fully scriptable or callable via CLI

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## Installation

```bash
pip install simulate_damage

## Example usage

simulate_damage \
  --r1 sample_R1.fastq.gz \
  --r2 sample_R2.fastq.gz \
  --out_r1 damaged_R1.fastq.gz \
  --out_r2 damaged_R2.fastq.gz \
  --ct5 0.03 --ctint 0.4 --ga3 0.01 --gaint 0.7 --overhang 10

