genbank_to

Contents:

  • Installation
    • Using Conda (Recommended)
    • Using pip
    • From Source (Development)
    • Dependencies
    • Verifying Installation
    • Testing Your Installation
    • Troubleshooting
      • ImportError: No module named ‘GenBankToLib’
      • Command not found: genbank_to
      • BioPython version issues
    • Upgrading
    • Uninstalling
  • Quick Start
    • Basic Usage
    • Common Conversions
      • Extract Genome Sequence
      • Extract Protein Sequences
      • Extract ORF Sequences (DNA)
      • Generate GFF3 File
      • Multiple Outputs at Once
    • Using as a Python Library
      • Extract All Protein Sequences
      • Extract Genome Sequences
      • Extract Functions
      • Convert to JSON Format
    • Example Workflow
    • Working with Multi-GenBank Files
      • Filtering by Sequence ID
    • Next Steps
  • Command-Line Usage
    • Basic Syntax
    • Required Arguments
    • Output Format Options
      • Nucleotide Outputs
      • Protein Outputs
      • Complex Format Outputs
      • Bakta JSON Metadata Options
    • Output Modifiers
    • Logging and Debugging
    • Other Options
    • Complete Example
  • Output Formats
    • FASTA Formats
      • Nucleotide FASTA (Genome)
      • ORF Nucleotide FASTA
      • Protein FASTA
    • Structured Formats
      • GFF3 (Generic Feature Format)
      • NCBI PTT Format
      • Function Table
    • Specialized Formats
      • Bakta JSON
      • AMRFinderPlus Format
      • Phage Finder Format
    • Output Modifiers
      • Separate Files
      • Sequence ID Filtering
      • Complex Headers
      • Compression
    • Format Comparison
  • Examples
    • Basic Examples
      • Convert GenBank to FASTA
      • Extract All Sequence Types
    • Working with Phage Genomes
      • Complete Phage Analysis
      • Phage Annotation Comparison
    • Bacterial Genome Analysis
      • Complete Bacterial Genome Conversion
      • AMR Analysis Pipeline
    • Multi-Genome Processing
      • Batch Processing
      • Processing Multi-Record Files
      • Extract Specific Chromosomes
    • Python Library Usage
      • Basic Library Import
      • Extract and Filter Proteins
      • Build Custom Function Database
      • Calculate Genome Statistics
      • Export to JSON Format
      • Merge Multiple Genomes
    • Advanced Examples
      • Complex Header Format
      • Include Pseudogenes
      • Compressed Output
      • Custom Logging
    • Integration Examples
      • BLAST Database Creation
      • Genome Browser Setup
      • Codon Usage Analysis
      • Phylogenetic Analysis
    • Troubleshooting Examples
      • Check File Format
      • Handle Gzipped Input
      • Extract from Failed Conversion
    • Performance Optimization
      • Large Genome Processing
      • Streaming Processing
  • API Reference
    • Core Functions
      • genbank_to_fna
      • genbank_to_faa
      • genbank_to_orfs
      • genbank_to_functions
      • genbank_to_ptt
      • genbank_to_gff
      • genbank_to_phage_finder
      • genbank_to_amrfinder
      • genbank_to_json
      • genbank_seqio
    • Utility Functions
      • feature_id
      • is_gzip
    • Data Structures
      • Bacteria Module
    • Version Information
    • Advanced Usage
      • Processing Large Files
      • Custom Processing Pipeline
      • Working with BioPython
    • Error Handling
    • Type Hints
  • Contributing
    • Getting Started
    • How to Contribute
      • Reporting Bugs
      • Suggesting Enhancements
      • Adding Output Formats
    • Code Contributions
      • Making Changes
    • Style Guidelines
      • Python Code Style
      • Docstring Format
    • Testing Guidelines
      • Writing Tests
      • Test Data
    • Documentation Guidelines
      • Documentation Structure
      • Building Documentation
      • Documentation Style
    • Pull Request Process
    • Code of Conduct
    • Communication
    • Recognition
    • Thank You!
    • Questions?
  • Changelog
    • Version History
      • Development Version
      • Previous Releases
    • Recent Updates
      • New Features
      • Improvements
      • Bug Fixes
    • Migration Notes
      • From NCBI Downloads to genbank_to
      • From deprekate/genbank
    • Citation
    • Roadmap
      • Planned Features
      • Request a Feature
      • Contributing
    • Versioning
    • Support
      • Getting Help
      • Reporting Issues
    • Security
    • License
    • Acknowledgments
genbank_to
  • Search

© Copyright 2024, Rob Edwards.

Built with Sphinx using a theme provided by Read the Docs.