scikit-bio
Primes
| scikit-bio | Primes | |
|---|---|---|
| 2 | 45 | |
| 833 | 2,362 | |
| 0.8% | 0.6% | |
| 8.8 | 7.0 | |
| 7 days ago | about 2 months ago | |
| Python | C# | |
| BSD 3-clause "New" or "Revised" License | - |
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scikit-bio
- What are some of the bioinformatic projects I could do on python as a beginner?
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Why I Use Nim instead of Python for Data Processing
You make a fair point that using optimized numerical libraries instead of string methods will be ridiculously fast because they're compiled anyway. For example, scikit-bio does just this for their reverse complement operation [1]. However, they use an 8 bit representation since they need to be able to represent the extended IUPAC notation for ambiguous bases, which includes things like the character N for "aNy" nucleotide [2]. One could get creative with a 4 bit encoding and still end up saving space (assuming you don't care about the distinction between upper versus lowercase characters in your sequence [2]). Or, if you know in advance your sequence is unambiguous (unlikely in DNA sequencing-derived data) you could use the 2 bit encoding. When dealing with short nucleotide sequences, another approach is to encode the sequence as an integer. I would love to see a library—Python, Nim, or otherwise—that made using the most efficient encoding for a sequence transparent to the developer.
[1] https://github.com/biocore/scikit-bio/blob/b470a55a8dfd054ae...
[2] https://en.wikipedia.org/wiki/Nucleic_acid_notation
[3]
Primes
- Primes – A Software Drag Race
- Is this an efficient way to check if a number is prime number?
- I need some help on a project!!!
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Has anyone solved the prime number problem on SPOJ yet using pure python?
Take a look at Dave Plummer’s Prime Sieve project.
- Top 5 Fastest Programming Languages: Rust, C++, Swift, Java, and 90 more compared!
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Zig wins Dave Plummer's prime sieve benchmark ... but via a problematic metric
There's a dedicated and quite cool website where you can browse the benchmark results: https://github.com/PlummersSoftwareLLC/Primes
- Since when did Python haters spread out everywhere? Maybe DNF5 would be faster because of ditched it, maybe.
- creating a vec takes forever?
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Python vs. Nodejs vs. Lua
Should look into Software Drag Racing https://github.com/PlummersSoftwareLLC/Primes
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We wouldn’t even consider writing back-end code for a website CMS in anything other than C, and we certainly wouldn’t use any of the interpreted languages that have sprung up in the last couple of decades and positioned themselves as the de facto go-to standards for web development.
Compiler WTF??? Can't you just use xxd to turn a hexdump into a binary like a real programmer would do?!?
What are some alternatives?
PrimesResult - The results of the Dave Plummer's Primes Drag Race
primesieve - 🚀 Fast prime number generator
nimpylib - Some python standard library functions ported to Nim
nimtorch - PyTorch - Python + Nim
RoaringBitmap - A better compressed bitset in Java: used by Apache Spark, Netflix Atlas, Apache Pinot, Tablesaw, and many others
viroiddb - A curated database of all available viroid-like RNA sequences
Mudlet - ⚔️ A cross-platform, open source, and super fast MUD client with scripting in Lua
biofast - Benchmarking programming languages/implementations for common tasks in Bioinformatics
LMRTFY - Let Me Run That For You: A C++20 Thread Pool Library
RecursiveFactorization.jl
zig - General-purpose programming language and toolchain for maintaining robust, optimal, and reusable software.