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//! [](https://github.com/althonos/uniprot.rs/stargazers) //! //! *Rust data structures and parser for the [UniprotKB database(s)].* //! //! [UniprotKB database(s)]: https://www.uniprot.org/ //! //! [](https://travis-ci.com/althonos/uniprot.rs/branches) //! [](https://codecov.io/gh/althonos/uniprot.rs) //! [](https://choosealicense.com/licenses/mit/) //! [](https://github.com/althonos/uniprot.rs) //! [](https://crates.io/crates/uniprot) //! [](https://docs.rs/uniprot) //! [](https://github.com/althonos/uniprot.rs/blob/master/CHANGELOG.md) //! [](https://github.com/althonos/uniprot.rs/issues) //! //! //! # 🔌 Usage //! //! The `uniprot::parse` function can be used to obtain an iterator over the entries //! of a UniprotKB database in XML format (either SwissProt or TrEMBL). It //! will use the [`uniprot::Parser`], which is either [`SequentialParser`] //! or [`ThreadedParser`] depending on the compilation features. //! //! ```rust //! extern crate uniprot; //! //! let f = std::fs::File::open("tests/uniprot.xml") //! .map(std::io::BufReader::new) //! .unwrap(); //! //! for r in uniprot::parse(f) { //! let entry = r.unwrap(); //! // ... process the Uniprot entry ... //! } //! ``` //! //! `uniprot::parse` takes any [`BufRead`] implementor as an input. Additionaly, //! if compiling with the [`threading`] feature, it will require the input to //! be [`Send`] and `'static` as well. //! //! ## 📦 Decoding Gzip //! //! If parsing a Gzipped file, you can use [`flate2::read::GzDecoder`] or //! [`libflate::gzip::Decoder`] to decode the input stream, and then simply //! wrap it in a [`BufferedReader`]. Note that [`flate2`] has slightly better //! performance, but binds to C,, while [`libflate`] is a pure Rust //! implementation. //! //! ## 📧 Downloading from FTP //! //! Uniprot is available from the two following locations: [`ftp.ebi.ac.uk`] //! and [`ftp.uniprot.org`], the former being located in Europe while the //! latter is in the United States. The `ftp` crate can be used to open //! a connection and parse the databases on-the-fly: see the //! [`uniprot::parse`] example to see a code snippet. //! //! ## 📧 Downloading from HTTP //! //! If FTP is not available, note that the EBI FTP server can also be reached //! using HTTP at [`http://ftp.ebi.ac.uk`]. This allows using HTTP libraries //! instead of FTP ones to reach the release files. //! //! //! # 📝 Features //! //! ## `threading` //! //! _**enabled** by default_. //! //! The `threading` feature compiles the parser module in multi-threaded mode. //! This feature greatly improves parsing speed and efficiency, but removes //! any guarantee about the order the entries are yielded in. //! //! //! ## 📋 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/). //! //! //! [`http://ftp.ebi.ac.uk`]: http://ftp.ebi.ac.uk //! [`ftp.ebi.ac.uk`]: ftp://ftp.ebi.ac.uk //! [`ftp.uniprot.org`]: ftp://ftp.uniprot.org //! [`threading`]: #threading //! [`flate2`]: https://docs.rs/flate2/ //! [`flate2::read::GzDecoder`]: https://docs.rs/flate2/latest/flate2/read/struct.GzDecoder.html //! [`libflate`]: https://docs.rs/libflate/ //! [`libflate::gzip::Decoder`]: https://docs.rs/libflate/latest/libflate/gzip/struct.Decoder.html //! [`BufferedReader`]: https://doc.rust-lang.org/std/io/struct.BufReader.html //! [`Entry`]: ./model/struct.Entry.html //! [`uniprot::parse`]: ./fn.parse.html //! [`uniprot::Parser`]: ./type.Parser.html //! [`SequentialParser`]: ./parser/struct.SequentialParser.html //! [`ThreadedParser`]: ./parser/struct.ThreadedParser.html #![allow(unused_imports)] extern crate bytes; #[cfg(feature = "threading")] extern crate crossbeam_channel; extern crate fnv; #[macro_use] #[cfg(feature = "threading")] extern crate lazy_static; #[cfg(feature = "threading")] extern crate num_cpus; extern crate quick_xml; extern crate url; #[macro_use] pub mod parser; pub mod model; pub mod error; #[doc(inline)] pub use self::parser::Parser; use std::io::BufRead; /// Parse a Uniprot database XML file. /// /// # Example: /// ```rust,no_run /// let mut client = ftp::FtpStream::connect("ftp.uniprot.org:21").unwrap(); /// client.login("anonymous", "anonymous").unwrap(); /// /// let f = client.get("/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz").unwrap(); /// let dec = libflate::gzip::Decoder::new(f).unwrap(); /// let mut parser = uniprot::parse(std::io::BufReader::new(dec)); /// /// println!("{:#?}", parser.next()) /// ``` pub fn parse<B: BufRead>(reader: B) -> Parser<B> { Parser::new(reader) } #[cfg(test)] mod tests { use quick_xml::Error as XmlError; use crate::error::Error; use super::*; #[test] fn parse_swissprot_200() { let f = std::fs::File::open("tests/uniprot.xml").unwrap(); let entries = crate::parse(std::io::BufReader::new(f)) .collect::<Result<Vec<_>, _>>() .expect("entries should parse successfully"); assert_eq!(entries.len(), 200); } mod sequential { use super::*; use crate::parser::SequentialParser; #[test] fn parse_single_entry() { let f = std::fs::File::open("tests/uniprot.xml").unwrap(); SequentialParser::new(std::io::BufReader::new(f)) .next() .expect("an entry should be parsed") .expect("the entry should be parsed successfully"); } #[test] fn fail_unexpected_eof() { let txt = &b"<entry>"[..]; let err = SequentialParser::new(std::io::Cursor::new(txt)) .next() .expect("should raise an error") .unwrap_err(); match err { Error::Xml(XmlError::UnexpectedEof(_)) => (), other => panic!("unexpected error: {:?}", other), } } } #[cfg(feature = "threading")] mod threaded { use super::*; use crate::parser::ThreadedParser; #[test] fn parse_single_entry() { let f = std::fs::File::open("tests/uniprot.xml").unwrap(); ThreadedParser::new(std::io::BufReader::new(f)) .next() .expect("an entry should be parsed") .expect("the entry should be parsed successfully"); } #[test] fn fail_unexpected_eof() { let txt = &b"<entry>"[..]; let err = ThreadedParser::new(std::io::Cursor::new(txt)) .next() .expect("should raise an error") .unwrap_err(); match err { Error::Xml(XmlError::UnexpectedEof(_)) => (), other => panic!("unexpected error: {:?}", other), } } } }