Configuration Guide

VarAnnote uses YAML-based configuration with environment variable support for flexible setup.

Configuration File

Default configuration file: config.yaml

# Database Configuration
databases:
  priority: ["clinvar", "gnomad", "dbsnp", "cosmic"]

# API Configuration
api:
  rate_limit: 100
  timeout: 30

# Cache Configuration
cache:
  enabled: true
  ttl: 3600

# Output Configuration
output:
  format: "json"
  include_metadata: true

Environment Variables

Override configuration with environment variables:

export VARANNOTE_API_KEY="your_api_key"
export VARANNOTE_CACHE_TTL=7200
export VARANNOTE_OUTPUT_FORMAT="csv"

Configuration Manager

from varannote.utils.config_manager import ConfigManager

# Load configuration
config = ConfigManager()

# Access settings
api_key = config.get('api.key')
cache_ttl = config.get('cache.ttl', default=3600)

# Update settings
config.set('output.format', 'excel')
config.save()