gene-id-resolver 0.1.1 on Python PyPI

🧬 Gene ID Resolver v0.1.1

A comprehensive Python toolkit for converting between gene identifiers (Gene Symbol ↔ Ensembl ID ↔ Entrez ID) with intelligent handling of deprecated and ambiguous mappings.

✨ What's New in v0.1.1

📝 Enhanced PyPI package description for better discoverability
🎯 Improved README with comprehensive documentation
🏷️ Official Zenodo DOI for academic citations
🔗 Better integration with scientific workflows

🎯 Key Features

✅ Multi-Directional Conversion - Seamlessly convert between Gene Symbol, Ensembl ID, and Entrez ID
✅ Deprecated Gene Handling - Automatically maps 58,000+ outdated gene symbols to current identifiers
✅ Ambiguity Detection - Identifies and reports genes with multiple mappings
✅ Batch Processing - Process entire CSV/TSV files with a single command
✅ Smart Auto-Correction - Fixes common formatting issues (whitespace, case sensitivity)
✅ Comprehensive Database - 62,710 genes from Ensembl Release 109
✅ CLI + Python API - Use via command-line or integrate into your scripts

🚀 Quick Start

Installation:

pip install gene-id-resolver

Command-Line Usage:

# Convert a single gene
gene-convert convert TP53 symbol entrez

# Process a file
gene-convert convert-file input.csv output.csv gene_column symbol ensembl

Python API:

from gene_id_resolver import GeneResolver

resolver = GeneResolver()
result = resolver.convert('TP53', 'symbol', 'ensembl')
print(result.target_id)  # ENSG00000141510

📊 Technical Specifications

🗄️ Database Size: 18.3 MB SQLite with 62,710 gene mappings
📜 Deprecated Genes: 3.9 MB HGNC dataset with 58,083 historical mappings
🐍 Python Support: 3.8, 3.9, 3.10, 3.11, 3.12
📦 Dependencies: pandas, click, tqdm (minimal footprint)
✅ Test Coverage: 96.9% (31/32 comprehensive tests passing)

🔬 Use Cases

🧪 Harmonizing gene identifiers across multiple datasets
📊 Preparing data for pathway enrichment analysis (KEGG, Reactome)
🔄 Converting legacy gene lists to current nomenclature
🧬 Integrating RNA-seq results with genomic databases
📈 Standardizing biomarker panels for clinical research

📚 Documentation & Links

📦 PyPI Package: https://pypi.org/project/gene-id-resolver/
💻 GitHub Repository: https://github.com/tahagill/gene-id-resolver
🏷️ Zenodo DOI: https://doi.org/10.5281/zenodo.17547077
📖 Full Documentation: See README.md in repository

📖 Citation

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

@software{ahmad2025geneidresolver,
  author       = {Ahmad, Taha},
  title        = {Gene ID Resolver: A Python Toolkit for Gene Identifier Conversion},
  year         = 2025,
  publisher    = {Zenodo},
  version      = {v0.1.1},
  doi          = {10.5281/zenodo.17547077},
  url          = {https://doi.org/10.5281/zenodo.17547077}
}

👨‍💻 Author

Taha Ahmad

📧 tahagill99@gmail.com
💻 github.com/tahagill

📄 License

MIT License - see LICENSE file for details

Note: This release improves package metadata and documentation while maintaining the same robust functionality of v0.1.0. All core features remain stable and production-ready.

gene-id-resolver 0.1.1 v0.1.1 - Initial Release on Python PyPI