microbiorust 0.1.4

Python bindings for microbiorust, Microbiology friendly bioinformatics functions

microbiorust-py

Python bindings for microBioRust — a high-performance, modular bioinformatics toolkit written in Rust.

microBioRust is the core Rust Crate

microbiorust-py provides fast and memory-efficient bioinformatics functionality to Python users by leveraging the power of Rust, exposed through PyO3. This package aims to offer an alternative to libraries like Biopython, with a focus on speed, correctness, and extensibility.

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Features

• Fast parsers for GenBank and EMBL formats
• Output to GFF, FAA, and FFN
• Accurate feature extraction and translation
• Seamless Python API for easy integration into existing pipelines
• Built with Rust for safety and performance
• Fast parsers for BLAST in XML and tabular formats
• Fast parser for MSA alignments, subset, get_consensus
• Sequence metrics: hydrophobicity,amino_counts,amino_percentage

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Installation

Build the PyModule from source using maturin (recommended) - You will need to use the --features flag below:

pip install maturin
maturin develop --features extension-module

You can run

cargo test

which is the Rust test to see if the pyfunctions have been successfully added to the PyModule

Example usage in Python:

import microbiorust
result = microbiorust.gbk_to_faa("test_input.gbk")
for r in result:
   print(r)