seq-lang/seq: A high-performance, Pythonic language for bioinformatics

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A high-performance, Pythonic language for bioinformatics – GitHub – seq-lang/seq: A high-performance, Pythonic language for bioinformatics

Seq — a language for bioinformatics

Introduction

A strongly-typed and statically-compiled high-performance Pythonic language!

Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C/C++.

Think of Seq as a strongly-typed and statically-compiled Python: all the bells and whistles of Python, boosted with a strong type system, without any performance overhead.

Seq is able to outperform Python code by up to 160x. Seq can further beat equivalent C/C++ code by up to 2x without any manual interventions, and also natively supports parallelism out of the box. Implementation details and benchmarks are discussed in our paper.

Learn more by following the tutorial or from the cookbook.

Examples

Seq is a Python-compatible language, and the vast majority of Python programs should work without any modifications:

def check_prime ( n ): if n > 1 : for i in range ( 2 , n ): if n % i == 0 : return False…