Rust-Bio
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration. (by rust-bio)
pest
The Elegant Parser (by pest-parser)
Our great sponsors
Rust-Bio | pest | |
---|---|---|
9 | 42 | |
1,500 | 4,365 | |
2.7% | 2.0% | |
6.7 | 7.4 | |
19 days ago | 25 days ago | |
Rust | Rust | |
MIT License | Apache License 2.0 |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Rust-Bio
Posts with mentions or reviews of Rust-Bio.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-01-01.
- Bioinformatics Data Structures in Rust
- Bioinformatics with Rust
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bioinformatic libraries and zig?
Does anyone know of zig native libraries for bioinformatics (here is a Rust example https://rust-bio.github.io/ )? It seems as though one could pull in a lot of bioinformatics C libraries such as done with https://github.com/brentp/hts-zig.
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Proteomics search engine written in Rust
e.g. Rust-Bio
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What are your top 3-5 programming languages and why?
I would start with the book and then rust-bio library. Rust is a pretty low level language compared to R/Python. It’s an especially good fit for writing efficient tools that make use of the kinds of algorithms / data structures that are implemented in rust-bio.
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I have to admit. The free code camp course is a bit more sparing than I would have preferred. How did everyone learn Rust?
Absolutely! It already is, e.g., https://github.com/rust-bio/rust-bio. I'm moving from the academia/nonprofit world into industry bioinformatics, and I intend to use Rust as much as possible. I've already replaced as much of my Python as possible with Rust. I feel I'm able to create larger, more complex programs with Rust because I have the compiler to keep me from making common mistakes that are so easy to make in dynamically typed languages like Perl and Python. It might take longer to write a program initially, but I've started to create a library of functions I can paste together to do things like parse a positive integer, find a bunch of files with a certain file extension, search through data for a pattern, parse CSV files, etc. Writing my latest book has provided even more common patterns I keep finding I use over and over.
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Is learning Rust and systems programming through the books Rust in Action and Crafting Interpreters a good idea?
I think there is huge potential for Rust in bioinformatics, and there are already some great projects like https://rust-bio.github.io/. It seems industry is also hiring for these skills. This Nature article is a little old, but also covers why people in the field are looking for greater safety and performance. It's relatively easy to write a Python program to do bio stuff, but it's also very easy to get lots of things wrong or for the resulting program to be slow and/or impossible to extend and maintain. In the long run, I think it makes sense to write in Rust. Perl was king in biofx when I started, and I would not have predicted it being displaced by Python, so there's good reason to believe that Python may one day be eclipsed by Rust.
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Whats your favourite open source Rust project that needs more recognition?
Well, someone mentioned https://rust-bio.github.io/
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How can one make Rust excel in the Sciences
So generally stuff in this maths/numerical space. The term is a bit deceptive because it rarely means domain-specific science libraries like rust-bio even thought that might be what you think when you hear "scientific computing".
pest
Posts with mentions or reviews of pest.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-12-06.
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nom > regex
And some related parser tools: - https://github.com/kevinmehall/rust-peg - https://github.com/pest-parser/pest - https://github.com/lalrpop/lalrpop
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Jasmine, A rust-like programming language that compiles to Java
I had recently completed the first year of my Computer Science class at school and will begin my second year soon. My schools' class forces the use of Java programming language, and I absolutely hated it. So, over the course of a little less than a month, I wrote my own programming language, in Rust (objectively best programming language), using pest, to be as similar to Rust as possible, but compiling to Java.
- Restoration of the pest3 work effort 🙌 · pest-parser/pest · Discussion #885
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What is the state of the art for creating domain-specific languages (DSLs) with Rust?
I second pest.rs. Using it is fairly intuitive and there's also a live playground on their website which is great for quickly developing and testing your AST (abstract syntax tree) parser for whatever language you're implementing.
- pest v2.6.0 released with a new meta-grammar feature (node tags)
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Finding a Crate to Help with Terminal Program Interface
This is where you'll run into trouble. People who write parsing-related Rust crates generally write things like pest that expect their syntax to be defined completely at compile time so the parser can be run through the compiler's optimizers for best performance.
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easy way to produce a parser
Give https://pest.rs a try.
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What is your opinion about lifetime of data generated from a parsing
For now I have used pest to generate an AST that borrows from the given input. But if I can manage to make the parser generic over the return type it may be worth a refactoring.
- Is there a parsing library (lexer?) which can handle generic tokens?
- v2.5.0: introducing `pest_debugger` · Discussion #739 · pest-parser/pest
What are some alternatives?
When comparing Rust-Bio and pest you can also consider the following projects:
dash - Data Apps & Dashboards for Python. No JavaScript Required.
nom - Rust parser combinator framework
kanidm - Kanidm: A simple, secure and fast identity management platform
lalrpop - LR(1) parser generator for Rust
clickhouse-rs - Asynchronous ClickHouse client library for Rust programming language.
rust-peg - Parsing Expression Grammar (PEG) parser generator for Rust
GeoRust - Geospatial primitives and algorithms for Rust
chumsky - Write expressive, high-performance parsers with ease.
Rhai - Rhai - An embedded scripting language for Rust.
pom - PEG parser combinators using operator overloading without macros.
cycle - Modern and safe symbolic mathematics
combine - A parser combinator library for Rust