perl-for-reysenbach-lab
hyperfine
| perl-for-reysenbach-lab | hyperfine | |
|---|---|---|
| 3 | 74 | |
| 3 | 20,020 | |
| - | - | |
| 10.0 | 8.1 | |
| over 1 year ago | 8 days ago | |
| Perl | Rust | |
| - | Apache License 2.0 |
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perl-for-reysenbach-lab
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Faster tetranucleotide (k-mer) frequencies!
I saw Jennifer's post about re-writing her perl scripts in python and how she saw a 2.5 times improvement.
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Calculating tetranucleotide (k-mer) frequencies
In 2016 I wrote a Perl script for the Reysenbach lab that calculates k-mer frequencies, for all k-mers in a given sequence. It was made public soon after, and you can find get_kmer_frequencies.pl on my Github page.
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Get GC Content
I wrote a Perl script that calculates GC content for all the sequences in a fasta file back in 2010 for the Reysenbach Lab, and it was made publicly available soon after. You can find get_gc_content.pl on GitHub (https://github.com/jmeneghin/perl-for-reysenbach-lab)
hyperfine
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Measuring startup and shutdown overhead of several code interpreters
Check out the official hyperfine Github repo
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Bun - The One Tool for All Your JavaScript/Typescript Project's Needs?
And then I used hyperfine to run the benchmarks on my MacBook Pro 14 M2 Max, and here are the results:
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Faster tetranucleotide (k-mer) frequencies!
Search "benchmarking tools for linux" and decide that hyperfine is good for what I'm doing. Run Jennifer's new python script against my refactored perl and find that the python is 1.26 times faster for k=3 and 1.47 times faster for k=4. For the Covid-19 sequence, these are both on the order of hundreds of milliseconds.
- Hyperfine: A command-line benchmarking tool
- FLaNK Weekly 08 Jan 2024
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Show HN: Inshellisense – IDE style shell autocomplete
> It is very possible to write sub 100ms procedures in TS, […]
I will not disagree with this statement because I don’t have a way to test inshellisense right now. Could you (or anyone with a working Node + NPM installation) please install inshellisense and post the actual numbers? Perhaps using a tool like hyperfine (https://github.com/sharkdp/hyperfine).
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Firefox has surpassed Chrome on Speedometer
Yeah, while it's not as thorough as these tools, the method is at least reproducible and sane, and with ~10 or so samples, you get an interval with a nice confidence.
Another through method will be hyperfine[0], yet I wanted to provide a method which requires no installation and can be done in a whim, without jumps and hoops, with the tools already at hand.
[0]: https://github.com/sharkdp/hyperfine
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How to optimize your config? What are mistakes to avoid when optimizing your config?
That is native and inbuild but I would suggest below options instead 1. Using lazy's Profile tab instead https://github.com/folke/lazy.nvim 2. Using a dedicated plugin to do this https://github.com/dstein64/vim-startuptime. 3. Using an external program hyperfine is one that I use https://github.com/sharkdp/hyperfine
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How to remove all <br> from all of my .html files
Fair enough, although might I recommend using hyperfine for your testing? ;p
What are some alternatives?
faster-perl-for-reysenbach - Tracks the progress of making old Perl scripts faster and more maintainable. Working from Meneghin's perl-for-reysenbach-lab repository of bioinformatics scripts.
criterion.rs - Statistics-driven benchmarking library for Rust
fd - A simple, fast and user-friendly alternative to 'find'
ripgrep - ripgrep recursively searches directories for a regex pattern while respecting your gitignore
awesome-mac - Now we have become very big, Different from the original idea. Collect premium software in various categories.
kubeconform - A FAST Kubernetes manifests validator, with support for Custom Resources!
quinn - Async-friendly QUIC implementation in Rust
quiche - 🥧 Savoury implementation of the QUIC transport protocol and HTTP/3
ble.sh - Bash Line Editor―a line editor written in pure Bash with syntax highlighting, auto suggestions, vim modes, etc. for Bash interactive sessions.
bat - A cat(1) clone with wings.
rust-gpu - 🐉 Making Rust a first-class language and ecosystem for GPU shaders 🚧
dust - A more intuitive version of du in rust