sriptype 0.1.0

SRIPType - A bioinformatics tool for 51k-SINE-RIP chip genotyping

SRIPType

A bioinformatics tool for 51k-SINE-RIP chip genotyping.

Installation

Method 1: Direct execution (clone and run)

git clone https://github.com/your-org/SRIPType.git
cd SRIPType

# Run via absolute path
/path/to/SRIPType/sriptype --help

# Or add to PATH
export PATH=/path/to/SRIPType:$PATH
sriptype --help

Method 2: pip install

git clone https://github.com/your-org/SRIPType.git
cd SRIPType
pip install .

sriptype --help

Method 3: Docker

# Build
docker build -t sriptype .

# Run
docker run --rm -v $(pwd):/data sriptype example -i /data/input.fasta -o /data/output.txt -t 4

Method 4: Conda (coming soon)

conda install -c your-channel sriptype

Usage

# Show help
sriptype --help

# Show version
sriptype --version

# Run a subcommand
sriptype example -i input.fasta -o output.txt -t 4

Global options

Option	Description
-v, --version	Show version and exit
-t, --threads INT	Number of threads (default: 1)
--verbose	Enable verbose output

Available subcommands

Subcommand	Description
example	Example subcommand (template)

Adding a new subcommand

1. Create a new Python file in sriptype_modules/subcommands/, e.g. mycommand.py
2. Define the following in the module:

"""My new subcommand."""

from sriptype_modules.utils import check_file_exists, ensure_output_dir, setup_logger

logger = setup_logger(__name__)

DESCRIPTION = "Description of my subcommand"


def add_arguments(parser):
    """Add subcommand-specific arguments."""
    parser.add_argument("-i", "--input", required=True, help="Input file")
    parser.add_argument("-o", "--output", required=True, help="Output file")


def run(args):
    """Execute the subcommand."""
    input_file = check_file_exists(args.input)
    output_file = ensure_output_dir(args.output)
    threads = args.threads

    # Your logic here
    logger.info("Done!")

3. The subcommand will be automatically discovered and available as sriptype mycommand.

Project Structure

SRIPType/
├── sriptype                      # Executable entry point
├── sriptype_modules/             # Core Python package
│   ├── __init__.py               # Version info
│   ├── cli.py                    # CLI argument parsing
│   ├── core.py                   # Core shared logic
│   ├── utils.py                  # Utility functions
│   └── subcommands/              # Subcommand modules
│       ├── __init__.py
│       └── example.py            # Example/template subcommand
├── tests/                        # Test directory
├── setup.py                      # Package setup
├── pyproject.toml                # Modern Python packaging config
├── requirements.txt              # Dependencies
├── Dockerfile                    # Docker build file
├── conda/meta.yaml               # Conda recipe
├── LICENSE
└── README.md

License

MIT License