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
Index
Index