📦🧬 nafcodec
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Rust coder/decoder for Nucleotide Archive Format (NAF) files.
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🗺️ Overview
Nucleotide Archive Format is a file
format proposed in Kryukov et al.[1] in 2019 for storing
compressed nucleotide or protein sequences combining 4-bit encoding and
Zstandard compression. NAF files can
be compressed and decompressed using the
original C implementation.
This library provides PyO3 bindings to the nafcodec
crate,
a Rust implementation of a NAF decoder using nom
for parsing the binary format, and zstd
for
handling Zstandard decompression. It provides a complete API that allows
iterating over the contents of a NAF file.
This is the Python version, there is a Rust crate 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.
- file-like decoding: Allow the decoder to read from a file-like object
instead of expecting a path.
The following features are planned:
- optional decoding: Allow the decoder to skip the decoding of certains
fields, such as ignoring quality strings when they are not needed.
- encoder: Implement an encoder as well, using either in-memory buffers
or temporary files to grow the archive.
🔌 Usage
Use a nafcodec.Decoder
to iterate over the contents of a Nucleotide Archive
Format, reading from the given path-like
or file-like object:
import nafcodec
decoder = nafcodec.Decoder("../data/LuxC.naf")
for record in decoder:
print(record.id)
All fields of the obtained Record
are optional, and actually depend on the
kind of data that was compressed.
💭 Feedback
⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the GitHub issue
tracker 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
and provides a changelog
in the Keep a Changelog format.
⚖️ License
This library is provided under the open-source
MIT license. The
NAF specification
is in the public domain.
This project is in no way not affiliated, sponsored, or otherwise endorsed
by the original NAF authors. It was
developed by Martin Larralde during his PhD
project at the European Molecular Biology Laboratory
in the Zeller team.
📚 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