Installation

genbank_to can be installed in several ways depending on your needs and preferences.

Using Conda (Recommended)

This is the easiest and recommended method for most users:

mamba create -n genbank_to genbank_to
conda activate genbank_to
genbank_to --help

If you prefer using conda instead of mamba:

conda create -n genbank_to genbank_to
conda activate genbank_to
genbank_to --help

Using pip

You can install genbank_to from PyPI using pip. We recommend using a virtual environment:

# Create a virtual environment
python -m venv venv

# Activate the virtual environment
# On Linux/macOS:
source venv/bin/activate
# On Windows:
# venv\Scripts\activate

# Install genbank_to
pip install genbank_to

# Verify installation
genbank_to --help

From Source (Development)

If you want to contribute to genbank_to or use the latest development version:

# Clone the repository
git clone https://github.com/linsalrob/genbank_to.git
cd genbank_to

# Create a virtual environment
python -m venv venv
source venv/bin/activate

# Install in editable mode
pip install -e .

# Verify installation
genbank_to --help

Dependencies

genbank_to requires Python 3.9 or later and the following packages:

biopython (>=1.74): For parsing GenBank files
numpy (>=1.16.0): For numerical operations
pandas: For data manipulation
bcbio-gff (>=0.6.6): For GFF format support

These dependencies will be automatically installed when you install genbank_to using any of the methods above.

Verifying Installation

After installation, verify that genbank_to is correctly installed:

# Check version
genbank_to --version

# View help
genbank_to --help

You should see the version information and command-line options.

Testing Your Installation

You can test your installation with a sample GenBank file:

# Download test data
wget https://raw.githubusercontent.com/linsalrob/genbank_to/main/test/NC_001417.gbk

# Convert to FASTA
genbank_to -g NC_001417.gbk -n NC_001417.fna

# Check the output
head NC_001417.fna

Troubleshooting

ImportError: No module named ‘GenBankToLib’

This error occurs when genbank_to is not properly installed. Make sure you’ve activated your virtual environment and installed the package:

source venv/bin/activate  # or conda activate genbank_to
pip install genbank_to

Command not found: genbank_to

This happens when the installation directory is not in your PATH. If using a virtual environment, make sure it’s activated. If using conda, activate the environment:

conda activate genbank_to

BioPython version issues

If you encounter BioPython-related errors, ensure you have a compatible version:

pip install --upgrade biopython>=1.74

Upgrading

To upgrade to the latest version:

Using pip:

pip install --upgrade genbank_to

Using conda:

conda update genbank_to

Uninstalling

To uninstall genbank_to:

Using pip:

pip uninstall genbank_to

Using conda:

conda remove genbank_to