sassy-rs 0.1.1

Fast approximate string searching using SIMD

simd-sassy Python Bindings

This directory contains the Python interface for the simd-sassy sequence search library, powered by Rust and PyO3.

Installation

You can install the package using maturin:

maturin develop --features python

Or install from PyPI (once published):

pip install simd-sassy

Usage

A simple usage is as follows:

pattern = b"ATCGATCG"
text = b"GGGGATCGATCGTTTT"
# alphabet: ascii, dna, uipac
searcher = sassy.Searcher("dna")
matches = searcher.search(pattern, text, k=1)
for i, match in enumerate(matches):
    print(f"Match {i+1}:")
    print(f"    Start: {match.text_start}")
    print(f"    End: {match.text_end}")
    print(f"    Cost: {match.cost}")
    print(f"    Strand: {match.strand}")
    print(f"    CIGAR: {match.cigar}")

This finds 3 matches:

Match 1:
    Start: 4
    End: 12
    Cost: 0
    Strand: +
    CIGAR: 8=
Match 2:
    Start: 6
    End: 14
    Cost: 1
    Strand: -
    CIGAR: 6=X=
Match 3:
    Start: 2
    End: 10
    Cost: 1
    Strand: -
    CIGAR: X7=

Further options are sassy.Searcher(alpha=0.5) to allow overhang alignments, and sassy.Searcher("dna", rc=False) to disable reverse complements for DNA or IUPAC strings.

See example.py for a larger example.