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Seq – A programming language for computational genomics and bioinformatics

github.com

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Re: Seq – A programming language for computational genomics and bioinformatics

#11

Post by amelius »

bscphil wrote: post #6

> Seq is a Python-compatible language, and the vast majority of Python programs should work without any modifications > Seq is able to outperform Python code by up to 160x. So ... a reimplementation of Python that can outperform cpython by over 100 times? I know literally nothing about this project, but I have to say that rings pretty false for me. Hell, even PyPy has trouble with many applications. (Plus they're cla…

It's probably in the same sense that Numpy is much faster than doing matrix operations with pure Python arrays and Python for-loops.

Re: Seq – A programming language for computational genomics and bioinformatics

#12

Post by dunefox »

bscphil wrote: post #8
aldanor wrote: post #7

Earlier quoted context omitted.

I also know literally nothing about this particular project, but why not? If you support a small restricted subset of Python it's completely doable under certain conditions for specific types of programs . E.g., Numba can easily outperform Python 100-1000x in numerical applications (done it myself multiple times), simply because it jit-compiles the code by first translating it to LLVM IR.

> If you support a small restricted subset of Python That's why I quoted their claim that the "vast majority" of Python programs run unmodified . Even PyPy barely achieves that. To really get 100x performance over Python (and even supposedly beat C) with a compiler that works on most unmodified Python code would be an extraordinary achievement.

That seems misrepresenting the original points: it can run the vast majority of python programs unmodified AND in some cases outperform Python - not at the same time.

Re: Seq – A programming language for computational genomics and bioinformatics

#14

Post by dgb23 »

encode wrote: post #13

Also see this comparison between Julia's BioSequences and Seq by Jakob Nissen and Ben Ward: https://biojulia.net/post/seq-lang/

An interesting takeaway:

> So it appears the primary reason BioJulia code is slower than Seq code in these three benchmarks is that BioSequences.jl is doing important work for you that Seq is not doing. As scientists, we hope you value tools that spend the time and effort to validate inputs given to it rather than fail silently.

Reminds me of the myriads of Excel catastrophes.

Re: Seq – A programming language for computational genomics and bioinformatics

#15

Post by arc-in-space »

bscphil wrote: post #6

> Seq is a Python-compatible language, and the vast majority of Python programs should work without any modifications > Seq is able to outperform Python code by up to 160x. So ... a reimplementation of Python that can outperform cpython by over 100 times? I know literally nothing about this project, but I have to say that rings pretty false for me. Hell, even PyPy has trouble with many applications. (Plus they're cla…

> We show that many important and widely-used NGS algorithms can be made up to 160× faster than their Python counterparts as well as 2× faster than the existing hand-optimized C++ implementations

It seems it's better to think of this particular claim as "we made a C++ algorithm that is 2x faster than the previous SotA C++ algorithm" (with the help of a heavily optimized DSL).

Re: Seq – A programming language for computational genomics and bioinformatics

#18

Post by drocer88 »

bscphil wrote: post #6

> Seq is a Python-compatible language, and the vast majority of Python programs should work without any modifications > Seq is able to outperform Python code by up to 160x. So ... a reimplementation of Python that can outperform cpython by over 100 times? I know literally nothing about this project, but I have to say that rings pretty false for me. Hell, even PyPy has trouble with many applications. (Plus they're cla…

Look at the link: https://github.com/seq-lang/seq It says 96% of the code is C++ in the "Languages" box on the right. C ( and C++ and Rust) outperforms Python in benchmarks and certain optimized C code can do 160x over very naive Python. So this is very possible, though the routines tested are probably cherry picked for bragging rights.

Re: Seq – A programming language for computational genomics and bioinformatics

#19

Post by kasperset »

I like this idea. However to me it is similar to using à la carte tools/programs along with bash script or DSL such as Nextflow. More often these stand-alone programs are already written in compiled languages. I am sure Seq will allow to build customized programs as compared to scripting or gluing programs.

Re: Seq – A programming language for computational genomics and bioinformatics

#20

Post by f6v »

> 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.

A pitch most people doing applied bioinformatics won’t understand/appreciate.

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