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https://github.com/althonos/nafcodec
Rust coder/decoder for Nucleotide Archival Format (NAF) files.
https://github.com/althonos/nafcodec
bioinformatics naf nom-parser nucleotide-sequences rust-library
Last synced: 22 days ago
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Rust coder/decoder for Nucleotide Archival Format (NAF) files.
- Host: GitHub
- URL: https://github.com/althonos/nafcodec
- Owner: althonos
- License: mit
- Created: 2023-10-06T23:26:37.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-08-18T12:20:46.000Z (5 months ago)
- Last Synced: 2024-12-28T15:17:07.847Z (28 days ago)
- Topics: bioinformatics, naf, nom-parser, nucleotide-sequences, rust-library
- Language: Rust
- Homepage:
- Size: 3 MB
- Stars: 5
- Watchers: 2
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: COPYING
Awesome Lists containing this project
README
# 📦🧬 `nafcodec` [](https://github.com/althonos/nafcodec/stargazers)
*Rust coder/decoder for [Nucleotide Archive Format (NAF)](https://github.com/KirillKryukov/naf) files*.
[](https://github.com/althonos/nafcodec/actions)
[](https://app.codecov.io/gh/althonos/nafcodec)
[](https://choosealicense.com/licenses/mit/)
[](https://github.com/althonos/nafcodec)
[](https://git.embl.de/larralde/nafcodec/)
[](https://crates.io/crates/nafcodec)
[](https://docs.rs/nafcodec)
[](https://github.com/althonos/nafcodec/blob/master/CHANGELOG.md)
[](https://github.com/althonos/nafcodec/issues)
## 🗺️ Overview
[Nucleotide Archive Format](https://github.com/KirillKryukov/naf) is a file
format proposed in Kryukov *et al.*[\[1\]](#ref1) in 2019 for storing
compressed nucleotide or protein sequences combining 4-bit encoding and
[Zstandard](https://github.com/facebook/zstd) compression. NAF files can
be compressed and decompressed using the
[original C implementation](https://kirill-kryukov.com/study/naf).
This crate provides a Rust implementation of a NAF decoder, from scratch,
using [`nom`](https://crates.io/crates/nom) for parsing the binary format,
and [`zstd`](https://crates.io/crates/zstd) for handling Zstandard
decompression. It provides a complete API that allows iterating over
the contents of a NAF file.
*This is the Rust version, there is a [Python package](https://pypi.org/project/nafcodec) available as well.*
### 📋 Features
- **streaming decoder**: The decoder is implemented using different readers
each accessing a region of the compressed file, allowing to stream records
without having to decode full blocks.
- **optional decoding**: Allow the decoder to skip the decoding of certains
fields, such as ignoring quality strings when they are not needed.
- **flexible encoder**: The encoder is implemented using an abstract storage
interface for temporary data, which allows to keep sequence in memory or
inside a temporary folder.
### 🔌 Usage
Use a [`Decoder`](https://docs.rs/nafcodec/latest/nafcodec/struct.Decoder.html)
to iterate over the contents of a Nucleotide Archive Format,
reading from any [`BufRead`](https://doc.rust-lang.org/nightly/std/io/trait.BufRead.html) +
[`Seek`](https://doc.rust-lang.org/nightly/std/io/trait.Seek.html) implementor:
```rust
let mut decoder = nafcodec::Decoder::from_path("../data/LuxC.naf")
.expect("failed to open nucleotide archive");
for result in decoder {
let record = result.unwrap();
// .. do something with the record .. //
}
```
All fields of the obtained [`Record`](https://docs.rs/nafcodec/latest/nafcodec/data/struct.Record.html)
are optional, and actually depend on the kind of data that was compressed.
The decoder can be configured through a
[`DecoderBuilder`](https://docs.rs/nafcodec/latest/nafcodec/struct.DecoderBuilder.html)
to ignore some fields to make decompression faster, even if they are present
in the source archive:
```rust
let mut decoder = nafcodec::DecoderBuilder::new()
.quality(false)
.with_path("../data/phix.naf")
.expect("failed to open nucleotide archive");
// the archive contains quality strings...
assert!(decoder.header().flags().test(nafcodec::Flag::Quality));
// ... but we configured the decoder to ignore them
for result in decoder {
let record = result.unwrap();
assert!(record.quality.is_none())
}
```
## 💭 Feedback
### ⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the
[GitHub issue tracker](https://github.com/althonos/nafcodec/issues) if you
need to report or ask something. If you are filing in on a bug, please include
as much information as you can about the issue, and try to recreate the same
bug in a simple, easily reproducible situation.
## 📋 Changelog
This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
and provides a [changelog](https://github.com/althonos/nafcodec/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/). The
[NAF specification](https://github.com/KirillKryukov/naf/blob/master/NAFv2.pdf)
is in the public domain.
*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the [original NAF authors](https://github.com/KirillKryukov). 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).*
## 📚 References
- \[1\] Kirill Kryukov, Mahoko Takahashi Ueda, So Nakagawa, Tadashi Imanishi. "Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences". Bioinformatics, Volume 35, Issue 19, October 2019, Pages 3826–3828. [doi:10.1093/bioinformatics/btz144](https://doi.org/10.1093/bioinformatics/btz144)