Biallelic

A python libary to standardize biallelic inactivation analysis

• About
• Get started
  • Requirements
  • Installation
• Manifest Format Specification
  • File Structure
  • Metadata Section
  • Reference Section (ref)
  • Input Section (input)
  • Analyses Section (analyses)
  • Complete Example
  • Running Analysis
  • Advanced Topics
  • Validation
  • Best Practices
  • Manifest Template
• Test Run
  • Available Data
  • Running the tool
• Architecture Guide
• System Overview
• Core Components
• Data Flow
• Data Harmonization: The Core Design Pattern
• Module Organization
  • Core Package Structure
  • Core Classes
• Plugin Architecture
  • Input Drivers
  • Discovery Analyses
• Configuration Format
  • Manifest YAML Structure
  • Path Resolution
• Error Handling Strategy
• Extensibility Points
• Backward Compatibility
• Performance Considerations
• Design Patterns
• Testing Strategy
  • See Also
• API Reference
• Core Modules
  • Data Models Module (biallelic.models)
  • Orchestrator Module (biallelic.bi)
  • Logging Module (biallelic.logging)
  • Utilities Module (biallelic.misc)
• Development Guide
  • Project Structure
  • Setting Up Development Environment
  • Coding Standards
  • Adding New Features
  • Testing
  • Building Documentation
  • Creating a Release
  • Debugging
  • Common Tasks
  • Contributing Back
  • Resources
• Troubleshooting Guide
• Installation Issues
  • ModuleNotFoundError: No module named ‘biallelic’
  • ImportError: cannot import name ‘X’ from ‘biallelic’
• Manifest Issues
  • “sample_donors reference not found”
  • “genes reference not found”
  • “Driver XXX doesn’t implement YYY”
• File Path Issues
  • “File not found” error
  • “Permission denied” error
• Data Format Issues
  • “Empty reference_map”
  • Invalid data format in file
• Analysis Issues
  • “Analysis module not found”
• Memory Issues
  • “MemoryError” or “Killed” during analysis
• Performance Issues
  • “Analysis takes too long”
• Logging and Debugging
  • “ERROR: Analysis failed”
• Getting More Help
• Common Mistakes
  • See Also

Indexes and tables

• Index

• Module Index

• Search Page