Compressed DNA sequence representation

[!WARNING] This is an experimental implementation.

ganz implements a simple way to store DNA sequences in a compressed format:

from ganz import DnaSequence

dna = DnaSequence("ACGT")

It also makes getting the one-hot representation of the DNA sequence very fast:

dna.unpack_bits()
# array([[1, 0, 0, 0],
#        [0, 1, 0, 0],
#        [0, 0, 1, 0],
#        [0, 0, 0, 1]], dtype=uint8)

Installation

pip install ganz

# or 

pip install git+https://github.com/gtca/ganz.git

Building from source

To build from source, you'll need:

• Rust toolchain (install from rustup.rs)
• Python 3.8 or newer
• NumPy

Then:

# Clone the repository
git clone https://github.com/gtca/ganz.git
cd ganz

# Install development dependencies
pip install maturin pytest numpy

# Build and install in development mode
pip install -e .

# Run tests
pytest tests/
cargo test