Metadata-Version: 2.4
Name: opensxraw
Version: 0.2.2
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Rust
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
License-File: LICENSE
Summary: Python bindings for the OpenSXRaw SCIEX .wiff / .wiff.scan file parser
Keywords: mass-spectrometry,sciex,wiff,raw,proteomics
Home-Page: https://sigilweaver.app/opensxraw/
Author-email: Nathan Riley <git@nathanriley.com>
License: Apache-2.0
Requires-Python: >=3.8
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: Documentation, https://sigilweaver.app/opensxraw/docs/
Project-URL: Homepage, https://sigilweaver.app/opensxraw/
Project-URL: Issues, https://github.com/Sigilweaver/OpenSXRaw/issues
Project-URL: Source, https://github.com/Sigilweaver/OpenSXRaw

# OpenSXRaw

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> Part of the [OpenMassSpec](https://sigilweaver.app/openmassspec/docs/)
> stack for mass spectrometry raw-file access. Sibling readers:
> [OpenTFRaw](https://github.com/Sigilweaver/OpenTFRaw) (Thermo),
> [OpenWRaw](https://github.com/Sigilweaver/OpenWRaw) (Waters),
> [OpenTimsTDF](https://github.com/Sigilweaver/OpenTimsTDF) (Bruker),
> [OpenARaw](https://github.com/Sigilweaver/OpenARaw) (Agilent).

Rust and Python reader for SCIEX `.wiff`/`.wiff.scan` legacy mass
spectrometry data files, with no SCIEX SDK or software dependency.
Covers the TripleTOF and QTRAP instrument families.

Documentation: [sigilweaver.app/opensxraw/docs](https://sigilweaver.app/opensxraw/docs)

## Install

**Prefer [`openmassspec-io`](https://github.com/Sigilweaver/OpenMassSpec)
with the `sciex` feature** unless you need this parser standalone
(minimal dependencies, or building your own abstraction) - the umbrella
gives you format auto-detection, mzML conversion, and Arrow streaming
across all wired-in vendors for free:

```sh
cargo add openmassspec-io --features sciex
```

```sh
pip install openmassspec[sciex]
```

Standalone:

Rust:

```sh
cargo add opensxraw
```

Python:

```sh
pip install opensxraw
```

## Quickstart

Rust:

```rust
use opensxraw::reader::Reader;
use openmassspec_core::SpectrumSource;

let mut reader = Reader::open("sample.wiff")?;
for spectrum in reader.iter_spectra() {
    println!("{}: {} peaks", spectrum.native_id, spectrum.mz.len());
}
```

Python:

```python
import opensxraw

reader = opensxraw.RawReader("sample.wiff")
spectrum = reader.read_spectrum(0)
print(spectrum.ms_level, spectrum.retention_time_sec, len(spectrum.mz))
```

`Reader::open` (and `RawReader`) expects the paired `.wiff.scan` file to
sit alongside the `.wiff` file, with `.scan` appended to the `.wiff`
filename.

See the [docs site](https://sigilweaver.app/opensxraw/docs) for the full
guide, format specification, and API reference.

## License

Apache-2.0. See [LICENSE](LICENSE).

The format specification was developed by binary analysis of public
mass-spectrometry datasets (PRIDE accessions). See
[CORPUS.md](CORPUS.md) and [ATTRIBUTION.md](ATTRIBUTION.md).

