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raidx

High-performance FASTA file reader with Python bindings

raidx is a drop-in replacement for pyfaidx implemented in Rust, providing 2-4x faster performance for FASTA file operations while maintaining full API compatibility.

⚡ Performance

raidx is fast:

Operation pyfaidx (ms) raidx (ms) Speedup
🚀 File Opening 0.254 0.068 3.72x faster
🧬 Sequence Access 0.252 0.061 4.13x faster
✂️ Sequence Slicing 0.259 0.077 3.35x faster
🔍 get_seq Method 0.268 0.071 3.76x faster
🔄 Reverse Complement 0.287 0.071 4.03x faster
🔁 Sequence Iteration 0.299 0.097 3.08x faster
🎯 Random Access 3.403 1.172 2.90x faster

📊 Benchmarked on the hg38 human genome assembly with 1000 iterations per test

Installation

pip install .

Quick Start

raidx provides the same API as pyfaidx:

>>> from raidx import Fasta
>>> genome = Fasta('genome.fasta')
>>> genome
Fasta("genome.fasta")

# Access sequences like a dictionary
>>> genome['chr1'][1000:1100]  
>chr1:1001-1100
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC...

# Get sequence metadata
>>> seq = genome['chr1'][1000:1100]
>>> seq.name
'chr1'
>>> seq.start  # 1-based
1001
>>> seq.end    # 0-based  
1100

# String-like operations
>>> genome['chr1'][1000:1100].complement
>chr1 (complement):1001-1100
TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG...

>>> -genome['chr1'][1000:1100]  # reverse complement
>chr1 (complement):1100-1001
GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT...

# Method-based access
>>> genome.get_seq('chr1', 1001, 1100)
>chr1:1001-1100
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC...

# Iteration
>>> for record in genome:
...     print(f"{record.name}: {len(record)} bp")
chr1: 248956422 bp
chr2: 242193529 bp
...

Key Features

  • Drop-in replacement for pyfaidx - same API, same behavior
  • Memory-mapped I/O for efficient file access
  • Rust performance with Python convenience
  • Full compatibility with existing pyfaidx code
  • Comprehensive indexing (.fai files compatible with samtools)
  • Rich sequence objects with metadata and methods
  • String-like operations (slicing, reverse, complement)

API Compatibility

raidx implements the complete pyfaidx API:

# All pyfaidx features work identically
from raidx import Fasta

# Indexing and slicing  
genome = Fasta('genome.fasta')
genome['chr1'][1000:2000]
genome[0][:100]  # First sequence, first 100 bp

# Sequence operations
seq = genome['chr1'][1000:1100]
seq.complement
seq.reverse  
-seq  # reverse complement

# Method calls
genome.get_seq('chr1', 1000, 2000)
genome.keys()
len(genome)

# Iteration
for record in genome:
    print(record.name, len(record))

Benchmarking

raidx includes two benchmarking approaches for different use cases:

pytest-benchmark

Use the organized benchmarks/ directory with pytest-benchmark for development, CI/CD, and detailed performance analysis:

# Install benchmark dependencies
pip install -e ".[benchmark]"

# Run all benchmarks
pytest benchmarks/

# Run specific benchmark categories
pytest benchmarks/benchmark_file_ops.py      # File operations
pytest benchmarks/benchmark_sequence_ops.py  # Sequence operations

# Save and compare results
pytest benchmarks/ --benchmark-save=baseline
pytest benchmarks/ --benchmark-compare=baseline

Standalone Benchmarks

Use the small benchmark tool for quick performance comparisons on your own files:

# Benchmark your files
python benchmark_raidx.py your_genome.fasta

# Adjust benchmarking details
python benchmark_raidx.py genome.fasta --iterations 1000 --random-access 500

Why raidx? raidx provides the same familiar pyfaidx interface, but with the performance of Rust underneath. Perfect for the pipelines that need to scale.

Metadata

Release files for raidx 0.1.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for raidx 0.1.1
File Size Uploaded
raidx-0.1.1.tar.gz 32.5 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for raidx 0.1.1
File
raidx-0.1.1-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ x86-64 Details
raidx-0.1.1-pp311-pypy311_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-pp311-pypy311_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-pp311-pypy311_pp73-manylinux_2_12_i686.manylinux2010_i686.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.12+ x86-32 Details
raidx-0.1.1-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl PyPy 3.10 PyPy 3.10 7.3 Linux glibc 2.17+ x86-64 Details
raidx-0.1.1-pp310-pypy310_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl PyPy 3.10 PyPy 3.10 7.3 Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.10 PyPy 3.10 7.3 Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-pp310-pypy310_pp73-manylinux_2_12_i686.manylinux2010_i686.whl PyPy 3.10 PyPy 3.10 7.3 Linux glibc 2.12+ x86-32 Details
raidx-0.1.1-pp39-pypy39_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl PyPy 3.9 PyPy 3.9 7.3 Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.9 PyPy 3.9 7.3 Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ x86-64 Details
raidx-0.1.1-cp314-cp314-manylinux_2_12_i686.manylinux2010_i686.whl CPython 3.14 CPython 3.14 Linux glibc 2.12+ x86-32 Details
raidx-0.1.1-cp313-cp313t-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-cp313-cp313t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-cp313-cp313-win_amd64.whl CPython 3.13 CPython 3.13 Windows x86-64 Details
raidx-0.1.1-cp313-cp313-win32.whl CPython 3.13 CPython 3.13 Windows x86-32 Details
raidx-0.1.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-64 Details
raidx-0.1.1-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-cp313-cp313-manylinux_2_12_i686.manylinux2010_i686.whl CPython 3.13 CPython 3.13 Linux glibc 2.12+ x86-32 Details
raidx-0.1.1-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
raidx-0.1.1-cp313-cp313-macosx_10_12_x86_64.whl CPython 3.13 CPython 3.13 macOS 10.12+ x86-64 Details
raidx-0.1.1-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details
raidx-0.1.1-cp312-cp312-win32.whl CPython 3.12 CPython 3.12 Windows x86-32 Details
raidx-0.1.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64 Details
raidx-0.1.1-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-cp312-cp312-manylinux_2_12_i686.manylinux2010_i686.whl CPython 3.12 CPython 3.12 Linux glibc 2.12+ x86-32 Details
raidx-0.1.1-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
raidx-0.1.1-cp312-cp312-macosx_10_12_x86_64.whl CPython 3.12 CPython 3.12 macOS 10.12+ x86-64 Details
raidx-0.1.1-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details
raidx-0.1.1-cp311-cp311-win32.whl CPython 3.11 CPython 3.11 Windows x86-32 Details
raidx-0.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details
raidx-0.1.1-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-cp311-cp311-manylinux_2_12_i686.manylinux2010_i686.whl CPython 3.11 CPython 3.11 Linux glibc 2.12+ x86-32 Details
raidx-0.1.1-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
raidx-0.1.1-cp311-cp311-macosx_10_12_x86_64.whl CPython 3.11 CPython 3.11 macOS 10.12+ x86-64 Details
raidx-0.1.1-cp310-cp310-win_amd64.whl CPython 3.10 CPython 3.10 Windows x86-64 Details
raidx-0.1.1-cp310-cp310-win32.whl CPython 3.10 CPython 3.10 Windows x86-32 Details
raidx-0.1.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ x86-64 Details
raidx-0.1.1-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl CPython 3.10 CPython 3.10 Linux glibc 2.12+ x86-32 Details
raidx-0.1.1-cp310-cp310-macosx_11_0_arm64.whl CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
raidx-0.1.1-cp310-cp310-macosx_10_12_x86_64.whl CPython 3.10 CPython 3.10 macOS 10.12+ x86-64 Details
raidx-0.1.1-cp39-cp39-win_amd64.whl CPython 3.9 CPython 3.9 Windows x86-64 Details
raidx-0.1.1-cp39-cp39-win32.whl CPython 3.9 CPython 3.9 Windows x86-32 Details
raidx-0.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ x86-64 Details
raidx-0.1.1-cp39-cp39-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl CPython 3.9 CPython 3.9 Linux glibc 2.12+ x86-32 Details
raidx-0.1.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ x86-64 Details
raidx-0.1.1-cp38-cp38-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ ARMv7l Details
raidx-0.1.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ ARM64 Details
raidx-0.1.1-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl CPython 3.8 CPython 3.8 Linux glibc 2.12+ x86-32 Details

Total release size: 17.3 MB

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