genesummary 0.3.2

A comprehensive Python package for retrieving detailed gene information from multiple public databases

GeneInfo

A comprehensive Python package for retrieving detailed gene information from multiple public databases with robust error handling, batch processing capabilities, and modular architecture.

Features

GeneInfo provides access to comprehensive gene annotation data through a unified interface:

Core Gene Information

• Basic gene data - Gene symbols, Ensembl IDs, descriptions, genomic coordinates, biotypes
• Transcripts - All transcript variants with protein coding information and alternative splicing
• Genomic location - Chromosome coordinates, strand information, gene boundaries

Functional Annotation

• Protein domains - Domain architecture from UniProt with evidence codes
• Gene Ontology - GO terms and annotations (Biological Process, Molecular Function, Cellular Component)
• Pathways - Reactome pathway associations and pathway hierarchies
• Protein interactions - Dual-source protein-protein interaction networks:
  • BioGRID - Experimental evidence with PubMed references (requires API key)
  • STRING-db - Computational predictions + experimental evidence (no API key required)

Evolutionary Information

• Homologs - Paralogs and orthologs across species with similarity metrics
• Cross-species mapping - Gene orthology relationships and conservation scores

Clinical & Disease Data

• Clinical variants - ClinVar pathogenic and benign variants with clinical significance
• GWAS associations - Genome-wide association study data from EBI GWAS Catalog
• Disease phenotypes - OMIM disease associations and phenotypic descriptions

Advanced Features

• Batch processing - Concurrent processing of large gene lists (1000+ genes)
• API key management - Secure handling of NCBI Entrez and OMIM API keys via environment variables or CLI
• Graceful degradation - Works without API keys with limited functionality (no clinical/phenotype data)
• Rate limiting - Built-in API courtesy delays and error handling
• Rich CLI - Beautiful command-line interface with progress bars and tables
• Export formats - JSON, CSV output with detailed and summary views
• Real data only - No mock data fallbacks, returns null when data is inaccessible

Installation

Using uv (Recommended)

# Install from source
uv add git+https://github.com/chunjie-sam-liu/geneinfo.git

# Or clone and install locally
git clone https://github.com/chunjie-sam-liu/geneinfo.git
cd geneinfo
uv add -e .

Using pip

# Install from source
pip install git+https://github.com/chunjie-sam-liu/geneinfo.git

# Or clone and install locally
git clone https://github.com/chunjie-sam-liu/geneinfo.git
cd geneinfo
pip install -e .

Requirements

• Python 3.11+
• Internet connection for API access (offline mode available)

Quick Start

API Key Configuration

For accessing ClinVar (clinical variants), OMIM (phenotype data), and BioGRID (protein interactions), you'll need API keys:

1. Create a .env file in your project directory:

# API Keys for external services
OMIM_API_KEY="your_omim_api_key_here"
ENTREZ_API_KEY="your_entrez_api_key_here"
ENTREZ_EMAIL="[e-mail]"
BIOGRID_API_KEY="your_biogrid_api_key_here"

2. Get API keys:

   • OMIM API Key: Register at OMIM API
   • Entrez API Key: Register at NCBI API
   • BioGRID API Key: Register at BioGRID API

3. API key priority:

   • CLI arguments (highest priority)
   • Environment variables from .env file
   • None (graceful degradation - returns null data)

Python API

from geneinfo import GeneInfo

# Option 1: Use environment variables (recommended)
# Create .env file with API keys (see above)
gene_info = GeneInfo()

# Option 2: Provide API keys explicitly
gene_info = GeneInfo(
    email="[e-mail]",
    entrez_api_key="your_entrez_key",
    omim_api_key="your_omim_key",
    biogrid_api_key="your_biogrid_key"
)

# Option 3: Work without API keys (limited functionality)
gene_info = GeneInfo(
    email=None,
    entrez_api_key=None,
    omim_api_key=None,
    biogrid_api_key=None
)

# Get comprehensive information for a single gene
result = gene_info.get_gene_info("TP53")
print(f"Gene: {result['basic_info']['display_name']}")
print(f"Description: {result['basic_info']['description']}")
print(f"Chromosome: {result['basic_info']['seq_region_name']}")
print(f"Transcripts: {len(result['transcripts'])}")
print(f"GO terms: {len(result['gene_ontology'])}")
print(f"Pathways: {len(result['pathways'])}")
print(f"Protein interactions: {len(result['protein_interactions'])} (BioGRID + STRING-db)")
print(f"Clinical variants: {len(result['clinvar'])} (requires API key)")

# Batch process multiple genes with concurrent workers
genes = ["TP53", "BRCA1", "EGFR", "MYC", "KRAS"]
df = gene_info.get_batch_info(genes, max_workers=5)
print(df[['gene_symbol', 'chromosome', 'transcript_count', 'go_term_count']].head())

# Export detailed information to JSON
gene_info.export_detailed_info(genes, "detailed_results.json")

# Export to organized directory structure
gene_info.export_batch_to_directory(genes, "gene_data/", max_workers=5)

Advanced Usage

# Process large gene lists efficiently
with open("large_gene_list.txt") as f:
    gene_list = [line.strip() for line in f if line.strip()]

# Initialize with API keys for full functionality
gene_info = GeneInfo(
    email="[e-mail]",
    entrez_api_key="your_entrez_key",
    omim_api_key="your_omim_key",
    biogrid_api_key="your_biogrid_key"
)

# Batch processing with progress tracking
df = gene_info.get_batch_info(gene_list, max_workers=10)

# Filter successful results
successful = df[df['error'].isna()]
print(f"Successfully processed {len(successful)}/{len(gene_list)} genes")

# Access specific data types
for _, gene in successful.iterrows():
    detailed = gene_info.get_gene_info(gene['query'])

    # Protein domains
    if detailed['protein_domains']:
        print(f"\n{gene['gene_symbol']} protein domains:")
        for domain in detailed['protein_domains'][:3]:
            print(f"  - {domain['name']}: {domain['start']}-{domain['end']}")

    # Protein interactions (dual sources)
    if detailed['protein_interactions']:
        biogrid_interactions = [i for i in detailed['protein_interactions']
                              if i.get('source_database') == 'BioGRID']
        stringdb_interactions = [i for i in detailed['protein_interactions']
                               if i.get('source_database') == 'STRING-db']
        print(f"  - {len(biogrid_interactions)} BioGRID interactions (experimental)")
        print(f"  - {len(stringdb_interactions)} STRING-db interactions (computational)")

    # Clinical variants (requires Entrez API key)
    if detailed['clinvar']:
        pathogenic = [v for v in detailed['clinvar']
                     if 'pathogenic' in v.get('clinical_significance', '').lower()]
        print(f"  - {len(pathogenic)} pathogenic variants found")

# Working without API keys (limited functionality)
gene_info_limited = GeneInfo(
    entrez_api_key=None,
    omim_api_key=None,
    biogrid_api_key=None
)

# This will still work but return empty for clinical/phenotype data
result = gene_info_limited.get_gene_info("TP53")
print(f"Basic info available: {bool(result['basic_info'])}")
print(f"Protein interactions: {len(result['protein_interactions'])} (STRING-db only)")
print(f"Clinical variants: {len(result['clinvar'])} (empty without API key)")
print(f"OMIM phenotypes: {bool(result['phenotypes'])} (empty without API key)")

Command Line Interface

# Single gene information with rich output
geneinfo --gene TP53 --output tp53_info.json

# Using API keys via CLI arguments
geneinfo --gene TP53 --entrez-api-key YOUR_ENTREZ_KEY --omim-api-key YOUR_OMIM_KEY --biogrid-api-key YOUR_BIOGRID_KEY --output tp53_info.json

# Using environment variables (recommended - create .env file)
geneinfo --gene TP53 --output tp53_info.json

# Process multiple genes from file
geneinfo --file genes.txt --output results.csv

# Detailed information in JSON format
geneinfo --gene BRCA1 --detailed --output brca1_detailed.json

# Batch processing with custom workers and API keys
geneinfo --file large_gene_list.txt --workers 10 \
  --entrez-api-key YOUR_ENTREZ_KEY \
  --omim-api-key YOUR_OMIM_KEY \
  --biogrid-api-key YOUR_BIOGRID_KEY \
  --email [e-mail] \
  --output batch_results.csv

# Export to organized directory structure
geneinfo --file genes.txt --output-dir gene_analysis/ --workers 8

# Verbose output for debugging
geneinfo --gene TP53 --verbose --detailed --output tp53_debug.json

# Process Ensembl IDs
geneinfo --gene ENSG00000141510 --output tp53_ensembl.json

# Species-specific queries (when supported)
geneinfo --gene TP53 --species human --output tp53_human.json

# Check CLI help for all options
geneinfo --help

CLI Output Examples

The CLI provides beautiful, formatted output with:

• 📊 Progress bars for batch processing
• 🎨 Colored tables for gene information display
• ⚡ Real-time processing statistics
• 📝 Summary reports with success/failure counts
• 🔍 Verbose logging for troubleshooting

Input Formats & Output

Supported Input Formats

The package accepts multiple gene identifier formats:

• Gene symbols: TP53, BRCA1, EGFR (case-insensitive)
• Ensembl Gene IDs: ENSG00000141510, ENSG00000012048
• Mixed lists: Can process files containing both symbols and IDs

Output Formats

Summary CSV Output

query,gene_symbol,ensembl_id,chromosome,start_pos,end_pos,strand,transcript_count,go_term_count,pathway_count,interaction_count,clinvar_count,error
TP53,TP53,ENSG00000141510,17,7668421,7687490,-1,12,87,23,71,1043,
BRCA1,BRCA1,ENSG00000012048,17,43044295,43170245,-1,27,34,15,45,892,

Detailed JSON Output

{
  "query": "TP53",
  "basic_info": {
    "id": "ENSG00000141510",
    "display_name": "TP53",
    "description": "tumor protein p53",
    "seq_region_name": "17",
    "start": 7668421,
    "end": 7687490,
    "strand": -1,
    "biotype": "protein_coding"
  },
  "transcripts": [...],
  "protein_domains": [...],
  "gene_ontology": [...],
  "pathways": [...],
  "protein_interactions": [...],
  "paralogs": [...],
  "orthologs": [...],
  "clinvar": [...],
  "gwas": {...}
}

Directory Export Structure

gene_data/
├── summary.csv              # Overview of all processed genes
├── TP53_ENSG00000141510.json
├── BRCA1_ENSG00000012048.json
└── EGFR_ENSG00000073756.json

Data Sources & Architecture

Primary Data Sources

• 🧬 Ensembl - Gene annotation, transcripts, genomic coordinates, homologs
• 🔬 UniProt - Protein domains, functional annotations, protein features
• 🎯 Gene Ontology - GO term annotations and functional classifications
• 🛤️ Reactome - Biological pathways and pathway hierarchies
• 🏥 ClinVar - Clinical variant classifications and disease associations
• 🧪 EBI GWAS Catalog - Genome-wide association study results
• 💊 OMIM - Mendelian disorders and phenotype-genotype relationships
• 📚 MyGene.info - Enhanced gene annotation aggregation
• 🔗 BioGRID - Experimental protein-protein interactions with evidence
• 🌐 STRING-db - Computational + experimental protein interaction networks

Modular Fetcher Architecture

The package uses a modular design with specialized fetchers:

# Genomic data fetchers
from geneinfo.fetchers.genomic import EnsemblFetcher, MyGeneFetcher

# Protein data fetchers
from geneinfo.fetchers.protein import UniProtFetcher, StringDBFetcher, BioGRIDFetcher

# Functional annotation fetchers
from geneinfo.fetchers.functional import GOFetcher, ReactomeFetcher

# Clinical data fetchers
from geneinfo.fetchers.clinical import ClinVarFetcher, GwasFetcher, OMIMFetcher

Robust Error Handling

• 🔄 Graceful degradation - Returns null data when APIs are unavailable or API keys missing
• ⏱️ Rate limiting with respectful API usage
• 🛡️ SSL/TLS handling for various certificate configurations
• 📝 Comprehensive logging with different verbosity levels
• 🔍 Input validation for gene symbols and Ensembl IDs
• 🔑 API key management - Secure environment variable handling

Performance & Usage Examples

Performance Characteristics

• Throughput: ~100-500 genes/minute (network dependent)
• Concurrency: Configurable worker threads (default: 5, max recommended: 10)
• Memory: Efficient streaming processing for large gene lists
• Rate limiting: Built-in delays to respect API usage policies

Real-world Usage Examples

Cancer Gene Panel Analysis

# Process a cancer gene panel with API keys for clinical data
cancer_genes = ["TP53", "BRCA1", "BRCA2", "EGFR", "KRAS", "PIK3CA", "AKT1"]
gene_info = GeneInfo(
    email="[e-mail]",
    entrez_api_key="your_entrez_key",
    omim_api_key="your_omim_key",
    biogrid_api_key="your_biogrid_key"
)

results = gene_info.get_batch_info(cancer_genes)
# Filter for genes with clinical variants (requires Entrez API key)
cancer_variants = results[results['clinvar_count'] > 0]
print(f"Found clinical variants in {len(cancer_variants)} cancer genes")

# Analyze protein interaction networks
for gene in cancer_genes:
    detailed = gene_info.get_gene_info(gene)
    interactions = detailed['protein_interactions']
    if interactions:
        biogrid_count = len([i for i in interactions if i['source_database'] == 'BioGRID'])
        stringdb_count = len([i for i in interactions if i['source_database'] == 'STRING-db'])
        print(f"{gene}: {biogrid_count} experimental + {stringdb_count} predicted interactions")

Pathway Enrichment Preprocessing

# Prepare data for pathway analysis
gene_list = ["TP53", "MDM2", "CDKN1A", "BAX", "BBC3"]  # p53 pathway genes
detailed_results = [gene_info.get_gene_info(gene) for gene in gene_list]

# Extract GO terms for enrichment analysis
all_go_terms = []
for result in detailed_results:
    for go_term in result['gene_ontology']:
        all_go_terms.append({
            'gene': result['query'],
            'go_id': go_term['go_id'],
            'go_name': go_term['go_name'],
            'namespace': go_term['namespace']
        })

Large-scale Genomics Project

# Process GWAS significant genes (thousands of genes)
with open("gwas_significant_genes.txt") as f:
    gwas_genes = [line.strip() for line in f]  # 5000+ genes

# Process in batches with progress tracking
gene_info.export_batch_to_directory(
    gwas_genes,
    "gwas_gene_annotation/",
    max_workers=8
)
# Creates organized directory with individual files + summary

Development & Testing

Running Tests

# Install development dependencies
uv add --dev pytest pytest-cov pytest-asyncio

# Run test suite
uv run pytest

# Run with coverage
uv run pytest --cov=geneinfo --cov-report=html

Project Structure

geneinfo/
├── geneinfo/
│   ├── __init__.py          # Main package exports
│   ├── core.py              # GeneInfo main class
│   ├── cli.py               # Command-line interface
│   ├── mock_data.py         # Fallback data for offline mode
│   └── fetchers/            # Modular data fetchers
│       ├── base.py          # Base fetcher with common functionality
│       ├── genomic.py       # Ensembl, MyGene fetchers
│       ├── protein.py       # UniProt, STRING-db fetchers
│       ├── functional.py    # GO, Reactome fetchers
│       └── clinical.py      # ClinVar, GWAS, OMIM fetchers
├── tests/                   # Comprehensive test suite
├── examples/                # Usage examples and demos
├── docs/                    # Documentation (you are here!)
└── pyproject.toml          # Modern Python packaging

Contributing

1. Fork the repository
2. Create a feature branch: git checkout -b feature-name
3. Follow the coding standards in .github/copilot-instructions.md
4. Add tests for new functionality
5. Run the test suite: uv run pytest
6. Submit a pull request

Dependencies & Requirements

Core Dependencies

• Python 3.11+ - Modern Python features and type hints
• requests - HTTP client for API calls
• pandas - Data manipulation and analysis
• numpy - Numerical computing
• typer - CLI framework with rich features
• rich - Beautiful terminal output and progress bars
• biopython - Bioinformatics tools (for Entrez/ClinVar)
• mygene - Enhanced gene annotation client
• python-dotenv - Environment variable management for API keys

System Requirements

• Internet connection for API access
• API keys for full functionality (NCBI Entrez, OMIM, BioGRID)
• Sufficient memory for large gene lists (typically <1GB for 10,000 genes)
• Email address for ClinVar/NCBI Entrez access (required when using API keys)

Troubleshooting

Common Issues

API Access Problems

# Test API connectivity
geneinfo --gene TP53 --verbose

# Working without API keys (limited functionality)
geneinfo --gene TP53 --entrez-api-key=None --omim-api-key=None --output results.json

API Key Configuration

# Check if API keys are being loaded correctly
geneinfo --gene TP53 --verbose

# Set API keys via environment variables (recommended)
echo 'ENTREZ_API_KEY="your_key_here"' > .env
echo 'OMIM_API_KEY="your_key_here"' >> .env
echo 'BIOGRID_API_KEY="your_key_here"' >> .env
echo 'ENTREZ_EMAIL="[e-mail]"' >> .env

# Or pass via CLI
geneinfo --gene TP53 --entrez-api-key YOUR_ENTREZ_KEY --omim-api-key YOUR_OMIM_KEY --biogrid-api-key YOUR_BIOGRID_KEY --email [e-mail]

Large Gene List Processing

# For very large lists, reduce concurrent workers
geneinfo --file huge_gene_list.txt --workers 3 --output results.csv

# Process in smaller batches if memory is limited
split -l 1000 huge_gene_list.txt batch_

Getting Help

• 📖 Check the examples/ directory for usage patterns
• 🐛 Report issues on GitHub with verbose output logs
• 💬 Include gene lists and error messages in bug reports
• 📧 Use --verbose flag for detailed debugging information

License & Citation

License

MIT License - see LICENSE file for details.

Citation

If you use GeneInfo in your research, please cite:

@software{geneinfo2025,
  author = {Liu, Chunjie},
  title = {GeneInfo: Comprehensive Gene Information Retrieval},
  url = {https://github.com/chunjie-sam-liu/geneinfo},
  version = {0.1.0},
  year = {2025}
}

Acknowledgments

This package aggregates data from multiple public biological databases. Please also cite the original data sources in your publications:

• Ensembl: Cunningham et al. (2022) Nucleic Acids Research
• UniProt: The UniProt Consortium (2023) Nucleic Acids Research
• Gene Ontology: Aleksander et al. (2023) Genetics
• Reactome: Gillespie et al. (2022) Nucleic Acids Research
• ClinVar: Landrum et al. (2020) Nucleic Acids Research
• BioGRID: Oughtred et al. (2021) Nucleic Acids Research
• STRING: Szklarczyk et al. (2023) Nucleic Acids Research
• GWAS Catalog: Sollis et al. (2023) Nucleic Acids Research

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Author: Chunjie Liu Contact: chunjie.sam.liu.at.gmail.com Version: 0.1.0 Date: 2025-08-06