RNA-Seq Data Annotator

A robust Python tool for annotating RNA sequencing data using standardized ontologies and classification systems. This tool provides automated annotation capabilities while maintaining strict adherence to established scientific ontologies.

Features

• Support for multiple ontology formats (primarily OBO)
• Automated annotation using Gene Ontology (GO) and Sequence Ontology (SO)
• Comprehensive validation framework
• Detailed logging system
• Type-safe implementation
• CSV output support
• Extensible architecture for custom annotation rules
• Docker support for containerized deployment
• MongoDB integration for data persistence
• Redis caching for improved performance

Prerequisites

Local Installation

• Python 3.8+
• pandas
• typing
• logging

Docker Deployment

• Docker 20.10+
• Docker Compose 2.0+
• At least 8GB RAM
• 20GB free disk space

Installation

Local Installation

1. Clone the repository:

git clone https://github.com/imrobintomar/rna-seq-annotator.git
cd rna-seq-annotator

2. Install required packages:

pip install -r requirements.txt

Docker Deployment

1. Clone the repository:

git clone https://github.com/imrobintomar/rna-seq-annotator.git
cd rna-seq-annotator

2. Create necessary directories:

mkdir -p data ontologies output logs

3. Start the services:

docker-compose up -d

4. Verify services are running:

docker-compose ps

Usage

Local Usage

from rna_seq_annotator import RNASeqAnnotator

# Define ontology files
ontology_files = {
    'GO': 'path/to/gene_ontology.obo',
    'SO': 'path/to/sequence_ontology.obo'
}

# Initialize annotator
annotator = RNASeqAnnotator(ontology_files)

# Load and annotate sequences
sequence_data = pd.read_csv('your_rna_seq_data.csv')
annotated_data = annotator.annotate_sequence(
    sequence_data,
    required_ontologies=['GO', 'SO'],
    output_file='annotated_sequences.csv'
)

Docker Usage

1. Place your input files:

cp your_rna_seq_data.csv data/
cp gene_ontology.obo ontologies/
cp sequence_ontology.obo ontologies/

2. Run annotation:

docker-compose exec rna-seq-annotator python annotate.py \
    --input /app/data/your_rna_seq_data.csv \
    --output /app/output/annotated_sequences.csv

3. Access results:

ls output/

Docker Services

The Docker deployment includes three main services:

RNA-Seq Annotator

• Main application container
• Resource limits: 2 CPUs, 4GB RAM
• Mounted volumes for data, ontologies, output, and logs

MongoDB

• Persistent data storage
• Secure authentication enabled
• Port: 27017
• Resource limits: 1 CPU, 2GB RAM

Redis

• Caching layer
• Password protected
• Port: 6379
• Resource limits: 0.5 CPU, 1GB RAM

Environment Variables

RNA-Seq Annotator

• LOG_LEVEL: Logging level (default: INFO)
• MAX_WORKERS: Number of worker processes (default: 4)
• ONTOLOGY_DIR: Directory for ontology files
• OUTPUT_DIR: Directory for output files

MongoDB

• MONGO_INITDB_ROOT_USERNAME: MongoDB admin username
• MONGO_INITDB_ROOT_PASSWORD: MongoDB admin password
• MONGO_INITDB_DATABASE: Default database name

Redis

• REDIS_PASSWORD: Redis authentication password

Input Data Format

The tool expects RNA-seq data in CSV format with the following columns:

• sequence_id (required): Unique identifier for each sequence
• sequence (required): The RNA sequence data
• Additional metadata columns (optional)

Example:

sequence_id,sequence,tissue_type,condition
seq001,AUGCAUGCAUGC,liver,control
seq002,GCAUGCAUGCAU,liver,treated

Output Format

The tool generates annotated data in CSV format with additional columns for each ontology:

• Original columns
• GO_annotation: Gene Ontology annotations
• SO_annotation: Sequence Ontology annotations
• validation_status: Validation results (if validation is performed)

Customization

Adding New Ontologies

1. Prepare your ontology file in OBO format
2. Add the ontology to the ontology_files dictionary:

ontology_files = {
    'GO': 'gene_ontology.obo',
    'SO': 'sequence_ontology.obo',
    'YOUR_ONTOLOGY': 'your_ontology.obo'
}

Docker Customization

Modify docker-compose.yml to adjust:

• Resource limits
• Volume mounts
• Environment variables
• Network configuration

Logging

The tool provides comprehensive logging with different levels:

• INFO: General operation information
• WARNING: Non-critical issues
• ERROR: Critical issues that need attention
• DEBUG: Detailed information for debugging

Logs are available:

• Local deployment: rna_seq_annotator.log
• Docker deployment: /app/logs/rna_seq_annotator.log

Troubleshooting

Docker Issues

1. Check service status:

docker-compose ps

2. View logs:

docker-compose logs [service-name]

3. Restart services:

docker-compose restart [service-name]

Contributing

1. Fork the repository
2. Create your feature branch (git checkout -b feature/AmazingFeature)
3. Commit your changes (git commit -m 'Add some AmazingFeature')
4. Push to the branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

License

This project is licensed under the MIT License

Citation

If you use this tool in your research, please cite:

@software{rna_seq_annotator,
  author = {Robin Tomar},
  title = {RNA-Seq Data Annotator},
  year = {2024},
  url = {https://github.com/imrobintomar/rna-seq-annotator}
}

Support

For support:

• Open an issue in the GitHub repository
• Contact [itsrobintomar@gmail.com]
• Check the troubleshooting guide

Acknowledgments

• Gene Ontology Consortium
• Sequence Ontology Project
• Contributors and maintainers of dependent packages
• Docker and container ecosystem contributors