Metadata-Version: 2.4
Name: gene-id-resolver
Version: 0.1.0
Summary: Production-grade gene ID conversion tool with comprehensive deprecated gene support
Author-email: Taha Ahmad <tahagill99@gmail.com>
License-Expression: MIT
Project-URL: Homepage, https://github.com/tahagill/gene-id-resolver
Project-URL: Documentation, https://github.com/tahagill/gene-id-resolver#readme
Project-URL: Repository, https://github.com/tahagill/gene-id-resolver
Project-URL: Bug Reports, https://github.com/tahagill/gene-id-resolver/issues
Keywords: bioinformatics,genomics,gene-ids,ensembl,gene-conversion,hgnc,deprecated-genes
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas>=1.5.0
Requires-Dist: click>=8.1.0
Requires-Dist: tqdm>=4.64.0
Provides-Extra: dev
Requires-Dist: pytest>=7.0.0; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: black>=22.0.0; extra == "dev"
Requires-Dist: flake8>=5.0.0; extra == "dev"
Dynamic: license-file

# gene-id-resolver

**The definitive gene ID conversion tool for reproducible bioinformatics**

> Born from the frustration of inconsistent gene mappings in multi-omics research

## Features

- 🔄 **Reproducible conversions** - version-controlled gene annotations
- 🕵️ **Ambiguity intelligence** - don't silently drop problematic genes  
- 📊 **Complete audit trails** - know exactly why each conversion succeeded/failed
- 💾 **Offline-first** - no API limits, no network dependencies

## Quick Start

```bash
pip install gene-id-resolver

from gene_id_resolver import Resolver

resolver = Resolver(genome_build="hg38", annotation_version="109")
result = resolver.convert(["MEF2C", "BRCA1"], from_type="symbol", to_type="ensembl")
print(result.audit_report)  


For Researchers
This tool solves the critical problem of gene identifier inconsistencies that plague reproducible bioinformatics analysis.

---

## 🔧 **GIT INITIALIZATION - PROPER VERSION CONTROL**

```bash
# Initialize Git
git init

# Add everything except ignored files
git add .

# Professional first commit
git commit -m "feat: initial project structure

- Modern pyproject.toml configuration
- Bioinformatics-optimized .gitignore
- Modular package structure
- Core dependencies for data engineering phase"

