#parser #uniprotkb #uniref #swissprot #trembl

uniprot

Rust data structures and parser for the Uniprot database(s)

8 releases (4 breaking)

0.5.1 Jan 11, 2022
0.5.0 Jan 11, 2022
0.4.0 Jul 24, 2021
0.3.1 Jan 19, 2020
0.1.1 Jan 15, 2020

#291 in Parser implementations

46 downloads per month

MIT license

175KB
4K SLoC

uniprot.rs Star me

Rust data structures and parser for the UniprotKB database(s).

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🔌 Usage

The uniprot::uniprot::parse function can be used to obtain an iterator over the entries of a UniprotKB database in XML format (either SwissProt or TrEMBL). XML files for UniRef and UniParc can also be parsed, with uniprot::uniref::parse and uniprot::uniparc::parse, respectively.

extern crate uniprot;

let f = std::fs::File::open("tests/uniprot.xml")
   .map(std::io::BufReader::new)
   .unwrap();

for r in uniprot::uniprot::parse(f) {
   let entry = r.unwrap();
   // ... process the Uniprot entry ...
}

Any BufRead implementor can be used as an input, so the database files can be streamed directly from their online location with the help of an HTTP library such as reqwest, or using the ftp library.

The XML format is the same for the EBI REST API and for the UniProt API, so this library can also be used to read single entries or larger queries. For instance, you can search UniProt for a keyword and retrieve all the matching entries:

extern crate ureq;
extern crate libflate;
extern crate uniprot;

let query = "bacteriorhodopsin";
let query_url = format!("https://www.uniprot.org/uniprot/?query={}&format=xml&compress=yes", query);

let req = ureq::get(&query_url).set("Accept", "application/xml");
let reader = libflate::gzip::Decoder::new(req.call().unwrap().into_reader()).unwrap();

for r in uniprot::uniprot::parse(std::io::BufReader::new(reader)) {
    let entry = r.unwrap();
    // ... process the Uniprot entry ...
}

See the online documentation at docs.rs for more examples, and some details about the different features available.

📝 Features

  • threading (enabled by default): compiles the multithreaded parser that offers a 90% speed increase when processing XML files.

🤝 Credits

uniprot.rs is developed and maintained by:

📋 Changelog

This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format.

📜 License

This library is provided under the open-source MIT license.

Dependencies

~2.8–4MB
~94K SLoC

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