spoars 0.1.0

Python bindings for spoars — partial order alignment consensus and MSA

spoars (Python)

Python bindings for spoars — a faithful, SIMD-accelerated native-Rust reimplementation of the spoa partial order alignment (POA) library, for consensus generation and multiple sequence alignment.

Install

pip install spoars

Usage

import spoars

# One-call convenience:
g = spoars.poa(["ACGTACGT", "ACGTTCGT", "ACGTACGT"])
print(g.consensus())  # "ACGTACGT"
print(g.msa())  # ['ACGTACGT', 'ACGTTCGT', 'ACGTACGT']

# Or build incrementally, with an alignment type and scoring:
g = spoars.Poa(alignment_type="global", scoring=spoars.Scoring.default())
for read in ["ACGTACGT", "ACGTTCGT", "ACGTACGT"]:
    g.add(read)
print(g.consensus(min_coverage=2))
print(g.gfa())  # GFA v1
print(g.dot())  # Graphviz DOT

alignment_type is one of "global", "local", or "overlap". Scoring takes (match, mismatch, gap_open, gap_extend, gap_open2, gap_extend2); the gap model (linear/affine/convex) is inferred, and Scoring.default() is spoa's convex default (5, -4, -8, -6, -10, -4).

Development

This package is built with maturin and developed with pixi:

pixi run develop      # build & install the extension into the dev env
pixi run test         # rebuild + pytest
pixi run format-check
pixi run lint
pixi run typecheck

License

MIT — see the repository.