OpenTimsTDF
Part of the OpenMassSpec stack for mass spectrometry raw-file access.
Rust and Python reader for timsTOF .d/ (TDF) acquisition bundles -
the SQLite analysis.tdf metadata file and the analysis.tdf_bin
binary frame stream. Runs on Linux, macOS, and Windows.
Documentation: sigilweaver.app/opentimstdf/docs
Install
Prefer openmassspec-io
with the bruker 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 bruker
pip install openmassspec[bruker]
Standalone:
Rust:
cargo add opentimstdf
Python:
pip install opentimstdf
Quickstart
Rust:
use opentimstdf::Reader;
let reader = Reader::open("my_bundle.d")?;
let calib = reader.calibration()?;
let frame = reader.frame(1)?;
for peak in reader.decode_peaks(&frame)? {
let mz = calib.tof_to_mz(peak.tof);
let im = calib.scan_to_inv_mobility(peak.scan);
println!("scan={} mz={:.4} 1/K0={:.4} i={}", peak.scan, mz, im, peak.intensity);
}
Python:
import opentimstdf
reader = opentimstdf.Reader("my_bundle.d")
calib = reader.calibration()
frame = reader.frame(1)
for peak in reader.decode_peaks(frame):
mz = calib.tof_to_mz(peak.tof)
print(peak.scan, mz, peak.intensity)
See the docs site for the full quickstart, guide, and format specification.
License
Apache-2.0. See LICENSE.
The TDF format and codecs were worked out from public sample data (PRIDE accessions). See ATTRIBUTION.md.
1 maintainer
Metadata
1 maintainer
Release files for opentimstdf 2.0.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| opentimstdf-2.0.0.tar.gz | 57.5 kB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| opentimstdf-2.0.0-cp38-abi3-win_amd64.whl | CPython 3.8 | abi3 | Windows x86-64 | Details |
| opentimstdf-2.0.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.8 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| opentimstdf-2.0.0-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.8 | abi3 | Linux glibc 2.17+ ARM64 | Details |
| opentimstdf-2.0.0-cp38-abi3-macosx_11_0_arm64.whl | CPython 3.8 | abi3 | macOS 11.0+ ARM64 | Details |
| opentimstdf-2.0.0-cp38-abi3-macosx_10_12_x86_64.whl | CPython 3.8 | abi3 | macOS 10.12+ x86-64 | Details |
Total release size: 7.9 MB
Release files / opentimstdf-2.0.0.tar.gz
| Download URL | opentimstdf-2.0.0.tar.gz |
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| Size | 57.5 kB |
| Tags | Source |
|
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| Size | 1.5 MB |
| Tags | CPython 3.8 Windows x86-64 abi3 |
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| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 abi3 |
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