OpenTFRaw
Part of the OpenMassSpec stack for mass spectrometry raw-file access.
Rust and Python reader for Thermo Fisher .raw mass spectrometry files,
covering format versions 8 through 66 (LCQ Classic through Orbitrap
Astral and modern TSQ).
Documentation: sigilweaver.app/opentfraw/docs
Install
Prefer openmassspec-io
with the thermo feature/extra 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:
cargo add openmassspec-io --features thermo
pip install openmassspec[thermo]
Standalone:
Rust:
cargo add opentfraw
Python:
pip install opentfraw
Quickstart
Rust:
use opentfraw::RawFileReader;
let raw = RawFileReader::open_path("sample.raw")?;
let mut file = std::fs::File::open("sample.raw")?;
for scan_num in 1..=raw.num_scans {
let peaks = raw.read_scan_peaks(&mut file, scan_num)?;
println!("scan {scan_num}: {} peaks", peaks.mz.len());
}
Python:
import opentfraw
raw = opentfraw.RawFile("run.raw")
mz, intensity = raw.peaks(3)
print(raw.scan(3)["filter_string"])
raw.to_mzml("run.mzML")
See the docs site for the full guide, format specification, and API reference.
Used by
| Project | Description |
|---|---|
| Mascope by Karsa Oy | Mass spectrometry data analysis platform using OpenTFRaw to ingest Thermo .raw files. |
License
Apache-2.0. See LICENSE.
The format specification was developed by binary analysis of public mass-spectrometry datasets (PRIDE accessions). See CORPUS.md and ATTRIBUTION.md.
1 maintainer
Release files for opentfraw 1.4.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| opentfraw-1.4.1.tar.gz | 96.2 kB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| opentfraw-1.4.1-cp38-abi3-win_amd64.whl | CPython 3.8 | abi3 | Windows x86-64 | Details |
| opentfraw-1.4.1-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.8 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| opentfraw-1.4.1-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.8 | abi3 | Linux glibc 2.17+ ARM64 | Details |
| opentfraw-1.4.1-cp38-abi3-macosx_11_0_arm64.whl | CPython 3.8 | abi3 | macOS 11.0+ ARM64 | Details |
| opentfraw-1.4.1-cp38-abi3-macosx_10_12_x86_64.whl | CPython 3.8 | abi3 | macOS 10.12+ x86-64 | Details |
Total release size: 2.2 MB
Release files / opentfraw-1.4.1.tar.gz
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| Size | 96.2 kB |
| Tags | Source |
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| Tags | CPython 3.8 Windows x86-64 abi3 |
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