# `uniprot.rs` [![Star me](https://img.shields.io/github/stars/althonos/uniprot.rs.svg?style=social&label=Star&maxAge=3600)](https://github.com/althonos/uniprot.rs/stargazers)

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

[UniprotKB database(s)]: https://www.uniprot.org/

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## 🔌 Usage

The [`uniprot::uniprot::parse`](https://docs.rs/uniprot/latest/uniprot/uniprot/fn.parse.html) 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`](https://docs.rs/uniprot/latest/uniprot/uniref/fn.parse.html)
and [`uniprot::uniparc::parse`](https://docs.rs/uniprot/latest/uniprot/uniparc/fn.parse.html), respectively.

```rust
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`](https://doc.rust-lang.org/stable/std/io/trait.BufRead.html)
implementor can be used as an input, so the database files can be streamed
directly from their [online location](https://www.uniprot.org/downloads) with
the help of an HTTP library such as [`reqwest`](https://docs.rs/reqwest), or
using the [`ftp`](https://docs.rs/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:

```rust
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`](https://docs.rs/uniprot) for more
examples, and some details about the different features available.

## 📝 Features

- [`threading`](https://docs.rs/uniprot/#threading) (_**enabled** by default_):
  compiles the multithreaded parser that offers a 90% speed increase when
  processing XML files.
- [`url-links`](https://docs.rs/uniprot/#url-links) (_**disabled** by default_):
  exposes the `links` in [`OnlineInformation`](https://docs.rs/uniprot/latest/uniprot/uniprot/comment/struct.OnlineInformation.html) as an [`url::Url`](https://docs.rs/url/latest/url/struct.Url.html).

## 🔍 See Also

If you're a bioinformatician and a Rustacean, you may be interested in these
other libraries:

- [`pubchem.rs`](https://github.com/althonos/pubchem.rs): Rust data structures
  and API client for the PubChem API.
- [`obofoundry.rs`](https://github.com/althonos/obofoundry.rs): Rust data
  structures for the OBO Foundry.
- [`fastobo`](https://github.com/fastobo/fastobo): Rust parser and abstract
  syntax tree for Open Biomedical Ontologies.
- [`proteinogenic`](https://github.com/althonos/proteinogenic): Chemical
  structure generation for protein sequences as
  [SMILES](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system) strings.

## 📋 Changelog

This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
and provides a [changelog](https://github.com/althonos/uniprot.rs/blob/master/CHANGELOG.md)
in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.


## 📜 License

This library is provided under the open-source
[MIT license](https://choosealicense.com/licenses/mit/).

*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the UniProt Consortium. It was developed
by [Martin Larralde](https://github.com/althonos/) during his PhD project
at the [European Molecular Biology Laboratory](https://www.embl.de/) in
the [Zeller team](https://github.com/zellerlab).*