I Use Nim Instead of Python for Data Processing

Re:I Use Nim Instead of Python for Data Processing by bionsystem on Friday September 06, 2024 @01:04AM (#41463057)

> import bioseq # my library, has k-mer iterator and FASTA parsing

I'm not a developer, but isn't that a bit unfair ? If one is going to rewrite all libs instead of just importing them from python, one is trading convenience for speed.

That said it's also mentioned that nim is compatible with python, does that mean it can import python libraries directly ?

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Re:I Use Nim Instead of Python for Data Processing by Gethsemane on Friday September 06, 2024 @04:53AM (#41464255)

It does seem like a bit of an unfair comparison. That being said, I am not aware of any k-mer python packages that have great performance. If k-mer counting performance was really important, I'd probably start to think about reaching for one of the more performant counters, such as KMC.

The real benefit of python in bioinformatics is the number of libraries available that let you interact with a bunch of software, perhaps do some light analysis, maybe make some pretty plots. And if you want to do some more intensive "useful" analysis, then all the ML packages, numpy, polars etc are quite hard to dismiss.

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Re:I Use Nim Instead of Python for Data Processing by leetnewb on Friday September 06, 2024 @03:44AM (#41463902)

There is nimpy (https://github.com/yglukhov/nimpy)

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