14 releases (breaking)
0.12.1 | Nov 5, 2024 |
---|---|
0.11.0 | Sep 4, 2023 |
0.10.0 | Dec 27, 2022 |
0.7.0+slow5lib.0.8.0 | Nov 2, 2022 |
0.3.1 | Mar 26, 2022 |
#41 in Biology
251 downloads per month
11MB
18K
SLoC
slow5-rs
A library for interacting with SLOW5/BLOW5 files in the Rust programming language.
For more information check out the main slow5lib repository or the paper.
This repository provides two crates:
slow5lib-sys
: Bindings to the C library usingbindgen
slow5
: Rust API built on-top ofslow5lib-sys
The interface for slow5
is largely stable and now updated primarily to follow new versions slow5lib
. If there is additional functionality you'd like to see, please file a Github Issue.
Installation
Add the following to your Cargo.toml
:
[dependencies]
slow5 = "0.12"
Git
If you'd like to download the git version, use the following command to download the repo
git clone --recursive https://github.com/bsaintjo/slow5-rs.git
Getting started
Reading signal from SLOW5 file
use slow5::{FileReader, RecordExt};
fn main() -> Result<(), Box<dyn std::error::Error>> {
let mut slow5 = FileReader::open("examples/example.slow5").unwrap();
for record in slow5.records() {
for signal in record?.picoamps_signal_iter() {
// Do stuff
}
}
Ok(())
}
Writing a compressed BLOW5 file with attributes
use std::error::Error;
use slow5::{FileWriter, SignalCompression, Record};
fn main() -> Result<(), Box<dyn Error>> {
let tmp_dir = std::env::temp_dir();
let output = tmp_dir.join("test.blow5");
let mut writer = FileWriter::options()
.signal_compression(SignalCompression::StreamVByte)
.attr("attribute", "value", 0)
.create(output)?;
let rec = Record::builder()
.read_id("test_id")
.read_group(0)
.digitisation(4096.0)
.offset(4.0)
.range(12.0)
.sampling_rate(4000.0)
.raw_signal(&[0, 1, 2, 3])
.build()?;
writer.add_record(&rec)?;
writer.close();
Ok(())
}
More example code
For more example code, see the test code. Several examples from the original library have been ported to rust and can be found in the examples directory.
Feature flags
zstd
: Enable zstd-based compression- enabled by default
zlib-ng
: Enable usage of high performance zlib-ng- adds
cmake
dependency
- adds
serde
: Enableserde
dependency- Mainly for serializing
Record
intoserde
-compatible formats
- Mainly for serializing
License
Licensed under either of
- Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
- MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)
at your option.
Contribution
Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.
Dependencies
~1–4MB
~83K SLoC