pybwa-lite 0.1.3

A lightweight Python implementation of the Burrows–Wheeler Aligner (BWA) with FM-index and multithreaded alignment.

🧬 PyBWA_lite — A Lightweight Burrows–Wheeler Aligner in Python

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🧠 Overview

PyBWA_lite is a pure-Python implementation of the Burrows–Wheeler Aligner (BWA) algorithm for fast, memory-efficient sequence alignment. It supports FM-index construction, banded Smith–Waterman extension, multithreaded alignment, and FASTQ I/O with quality scores — making it a compact, research-friendly alternative to native BWA for teaching, prototyping, and custom pipelines.

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✨ Features

✅ FM-Index Construction & Querying
Efficient Burrows–Wheeler Transform (BWT)–based indexing with rank/select operations for fast substring search and backward extension.

✅ Banded Smith–Waterman Extension
Optimized local alignment algorithm that restricts the search space to a diagonal band — improving speed without losing accuracy.

✅ Parallel Read Alignment
Multithreaded alignment engine supporting FASTA and FASTQ reads for high-throughput analysis.

✅ Quality-Aware FASTQ Parsing
Fully supports read qualities, enabling accurate scoring and filtering during alignment.

✅ SAM/BAM Output
Interoperable with the pysam library — easily write, parse, and manipulate alignment outputs.

✅ Command-Line Interface (CLI)
Use pybwa-lite directly from your terminal for quick indexing and read alignment tasks:

pybwa-lite index reference.fasta
pybwa-lite align reference.fmi reads.fastq -o output.sam


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### 🧩 Installation

#### From PyPI (once released)

```bash
pip install pybwa

From Source (Development)

git clone https://github.com/soumyapriyagoswami/pybwa.git
cd pybwa
pip install -e .

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⚙️ Quick Start

1️⃣ Build an Index

from pybwa_lite.index import build_index
fm = build_index("reference.fasta", out_path="ref_index.pkl")

2️⃣ Align Reads (Single or FASTQ)

from pybwa_lite.align import align_reads
results = align_reads("reads.fastq", "ref_index.pkl", threads=4)
for r in results:
    print(r)

3️⃣ Command-Line Usage

# Build index
pybwa_lite index reference.fasta -o ref_index.pkl

# Align reads
pybwa_lite align reads.fastq -x ref_index.pkl -t 4 -o output.sam

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🧠 Architecture Overview

Module	Description
index.py	Builds and loads FM-index structures for references
fmidx.py	Implements FM-index, suffix array, and BWT
align.py	Seeding, banded Smith–Waterman extension, multithreaded alignment
samtools.py	Utilities for SAM/BAM file handling using pysam
cli.py	Command-line interface for index building and alignment
tests/	Pytest-based unit tests for FM-index and alignment verification

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🧪 Running Tests

pytest -v

Expected output:

tests/test_alignment.py::test_single_read_alignment PASSED
tests/test_alignment.py::test_fastq_alignment_with_qualities PASSED
tests/test_alignment.py::test_multithreaded_alignment_consistency PASSED
tests/test_fmindex.py::test_suffix_array_sorted PASSED
tests/test_fmindex.py::test_backward_search_basic PASSED

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⚡ Performance Highlights

Feature	Description	Speedup
FM-index lookup	Optimized with prefix caching	~3× faster
Multithreading	Parallel read alignment	~N× faster (per thread)
Banded SW	Reduced dynamic programming table	~5× faster on long reads

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🧰 Dependencies

• numpy
• pysam
• tqdm
• pytest (for testing only)

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📦 Project Structure

pybwa/
├── __init__.py
├── align.py
├── cli.py
├── fmidx.py
├── index.py
├── samtools.py
tests/
├── test_alignment.py
├── test_fmindex.py

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🤝 Contributing

Contributions are welcome! If you have ideas for improving FM-index efficiency, integrating GPU kernels, or extending to RNA-seq workflows:

1. Fork this repo
2. Create a feature branch
3. Submit a pull request 🚀

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🧾 License

MIT License © 2025 Soumyapriya Goswami

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🌐 Links

🔗 GitHub Repository: soumyapriyagoswami/pybwa 📘 Documentation: Coming Soon 🐍 PyPI Package: (after release)