How to call Rust functions from Python code in JupyterLab

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Python is an important tool in any bioinformatician’s toolkit. My goal is to help you add Rust in this toolkit rather than replace Python. Here is a way to make sure your two tools can talk to each other.

Step 1: Install maturin (Rust crate)

cargo install maturin

Step 2: Create a new Rust project and add pyo3. Or add this dependency to an existing project.

cargo new rusty_python --lib 

// Add this in Cargo.toml file

[dependencies]
pyo3 = { version = "0.20", features = ["extension-module"] }

Step 3: Write new Rust functions that will be called from Python or modify existing ones.

// Example lib.rs file

use pyo3::prelude::*;

#[pyfunction]
fn gc_content(seq: &str) -> PyResult<f32> {
    let mut length = 0;
    let mut count = 0;
    for base in seq.chars() {
        length += 1;
        if base == 'G' || base == 'C' {
            count += 1;
        }
    }
    Ok(count as f32 / length as f32)
}

// This function name should be same as your project name
#[pymodule]
fn rusty_python(_py: Python, m: &PyModule) -> PyResult<()> {
    m.add_function(wrap_pyfunction!(gc_content, m)?)?;
    Ok(())
}

Step 4: Let maturin do its magic

Run the following command within your Rust project (inside rusty_python directory).

maturin develop

Step 5: Call your Rust function from Python

from rusty_python import gc_content

dna_sequence = "ACTG"

gc_content(dna_sequence)

# Output: 0.5

Next Steps

• See the Jupyter notebook that calls Rust from Python
• See the Rust project with a function designed to work with Python