semvec/pypi-packages huggingface dataset:
simulate-damage 0.1.4
Simulate ancient DNA deamination damage on paired-end FASTQ files
License: MIT
Requires Python: >=3.7

# 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.

---

##  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

---

## 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
pylint-mcp 0.1.2
MCP server providing pylint functionality
License: MIT
Requires Python: >=3.10

# Pylint MCP

An MCP server that runs pylint on a given file

## Features

- **lint**: Check a python file for syntactic errors using pylint.

## Prerequisites

- **Python**: Version 3.10 or greater
- **uv**: Package and dependency manager for Python projects.

## Installation

2. **Install Dependencies**:
   Add the required dependencies using `uv`:
   ```bash
   uv sync
   ```

## Usage

### Running the Server

Start the FastMCP server in development mode:
```bash
uv run mcp dev cli.py
```

### Installing to Claude Desktop

Install the server as a Claude Desktop application:
```bash
uv run mcp install cli.py --name "pylint"
```

Configuration file as a reference:

```json
{
   "mcpServers": {
       "pylint": {
           "command": "uvx",
           "args": [ "pylint-mcp" ]
       }
   }
}
```

### Available Tools

#### `lint`

Check a python file for syntactic errors using pylint.

**Parameters**:
- `filename` (str): The python source file to check for syntactic errors.

**Example**:
> Check `example.py` for syntactic errors

**Output**:
```
[
    {
        "type": "convention",
        "module": "example.cli",
        "obj": "",
        "line": 31,
        "column": 0,
        "endLine": null,
        "endColumn": null,
        "path": "example.py",
        "symbol": "line-too-long",
        "message": "Line too long (204/100)",
        "message-id": "C0301"
    },
    {
        "type": "error",
        "module": "example.cli",
        "obj": "",
        "line": 1,
        "column": 0,
        "endLine": 1,
        "endColumn": 17,
        "path": "example.py",
        "symbol": "import-error",
        "message": "Unable to import 'mcp'",
        "message-id": "E0401"
    }
]
```

## License

This project is licensed under the MIT License. See the [COPYING](COPYING) file for details.