genebank-file-generater 0.1.1

A comprehensive tool for converting DNA FASTA files to annotated GenBank format with automated gene prediction using Augustus

GbkGen - GenBank File Generator

A comprehensive tool for converting DNA FASTA files to annotated GenBank format with automated gene prediction using Augustus. GbkGen provides a command-line interface for flexible genomic data processing.

Features

• FASTA to GenBank Conversion: Convert DNA sequences from FASTA format to fully annotated GenBank files
• Automated Gene Prediction: Integrated Augustus gene prediction with support for multiple species models
• GFF File Support: Use existing GFF annotations or generate new ones with Augustus
• Multiprocessing Support: Parallel processing for large datasets with configurable CPU cores
• Multi-sequence Processing: Handle multiple DNA sequences in a single FASTA file
• Species-Specific Models: Configurable Augustus species models for accurate gene prediction
• Robust Error Handling: Comprehensive logging and error reporting
• File Validation: Automatic validation of input files and compatibility checking
• Temporary File Management: Automatic cleanup of intermediate files

Installation

Prerequisites

• Python 3.13 or higher
• Augustus gene prediction tool (installed and available in PATH)
• pip or uv package manager

Using UV (Recommended)

# Clone the repository
git clone https://github.com/darrengao628/genebank_file_generater
cd genebank_file_generater

# Install with uv
uv sync

Using pip

# Clone the repository
git clone https://github.com/darrengao628/genebank_file_generater
cd genebank_file_generater

# Install dependencies
pip install -r genebank_file_generater/requirements.txt

Augustus Installation

Make sure Augustus is installed and available in your PATH:

# For Ubuntu/Debian
sudo apt-get install augustus

# For macOS with Homebrew
brew install augustus

# Or build from source
# Follow instructions at: http://bioinf.uni-greifswald.de/augustus/

Usage

Command Line Interface

Basic Usage

If installed from source:

# Convert FASTA to GenBank (automatically creates input.gbk)
python -m genebank_file_generater.genebank_generater input.fasta

# With custom output filename
python -m genebank_file_generater.genebank_generater input.fasta -o output.gbk

# With specific species model
python -m genebank_file_generater.genebank_generater input.fasta -s human

# Using multiple CPU cores for faster processing
python -m genebank_file_generater.genebank_generater input.fasta -c 8

If installed via pip:

# Convert FASTA to GenBank (automatically creates input.gbk)
gbkgen input.fasta

# With custom output filename
gbkgen input.fasta -o output.gbk

# With specific species model
gbkgen input.fasta -s human

# Using multiple CPU cores for faster processing
gbkgen input.fasta -c 8

Automatic GFF File Detection

The program automatically detects corresponding GFF files:

• If input.fasta is provided, it looks for input.gff or input.gff3
• If found, the GFF file is used automatically (no need for -g flag)
• The output filename is always based on the input FASTA filename

# If 299.fa and 299.gff exist, this automatically uses 299.gff
python -m genebank_file_generater.genebank_generater 299.fa
# Creates 299.gbk as output

# Override automatic GFF detection with explicit GFF file
python -m genebank_file_generater.genebank_generater 299.fa -g custom.gff -o output.gbk

Advanced Usage

# Use existing GFF file instead of running Augustus
gbkgen input.fasta -g annotations.gff -o output.gbk

# Specify custom working directory
gbkgen input.fasta -w /tmp/augustus -o output.gbk

# Full example with all options
gbkgen input.fasta \
  --output output.gbk \
  --species aspergillus_fumigatus \
  --workdir ./augustus_output \
  --cpu 4

Command Line Options

Option	Short	Description	Default
input		Input DNA FASTA file (required)
--output	-o	Output GenBank file	input.gbk
--species	-s	Augustus species model	aspergillus_fumigatus
--workdir	-w	Working directory for Augustus	./augustus_output
--gff	-g	Pre-existing GFF3 file	None
--cpu	-c	Number of CPU cores	All available

Supported Species Models

GbkGen supports all Augustus species models. Common models include:

• aspergillus_fumigatus - Aspergillus fumigatus (default)

For a complete list, run:

augustus --species=help

Project Structure

GbkGen/
├── README.md                           # Main project documentation
├── pyproject.toml                      # Project configuration
├── main.py                             # Simple entry point
├── claude.md                           # Technical analysis
├── genebank_file_generater/            # Core conversion library
│   ├── __init__.py
│   ├── genebank_generater.py          # Main conversion logic
│   ├── gff_parser.py                  # GFF file parsing
│   ├── record.py                      # Record and feature management
│   ├── pyproject.toml                 # Package configuration
│   ├── requirements.txt               # Dependencies
│   ├── README.md                      # Package documentation
│   └── ToDO.md                        # Development roadmap
├── augustus_output/                   # Default Augustus output directory



### Getting Help
- Check the [Issues](https://github.com/darrengao628/genebank_file_generater/issues) page
- Review the [ToDO.md](genebank_file_generater/ToDO.md) for known limitations
- Create a new issue with detailed error information


## Changelog

### Version 0.1.0
- Initial release
- Core FASTA to GenBank conversion functionality
- Augustus integration with multiprocessing support
- GFF file parsing and validation
- Comprehensive error handling and logging
- Package distribution support with PyPI
- Simplified dependencies for easier installation


## Acknowledgments

- **BioPython** team for sequence handling libraries
- **Augustus** team for gene prediction software
- **antiSMASH** project for GFF parsing components


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For more information, visit the [project repository](https://github.com/darrengao628/genebank_file_generater) or contact the development team.