Crate mzdata

mzdata provides basic access to raw and processed mass spectrometry data formats in Rust.

For a guide, see the tutorial section.

The library currently supports reading:

1. MGF files using MGFReader in mzdata::io::mgf
2. mzML & indexedmzML files using MzMLReader in mzdata::io::mzml
3. mzMLb files using MzMLbReader in mzdata::io::mzmlb, if the mzmlb feature is enabled
4. Thermo RAW files using ThermoRawReader in mzdata::io::thermo, if the thermo feature is enabled

and writing:

1. MGF files using MGFWriter in mzdata::io::mgf
2. mzML & indexedmzML files using MzMLWriter in mzdata::io::mzml
3. mzMLb files using MzMLbWriter in mzdata::io::mzmlb, if the mzmlb feature is enabled

This menagerie of different formats and gzip compression or not can be inferred from a path or io::Read using io::infer_format and io::infer_from_stream. Conventional dispatch is possible through MZReader. The mz_read macro provides a convenient means of working with a value with zero added overhead, but with a limited scope. The mz_write macro is the equivalent for opening a writer. There are additional tools for dealing with file format dispatch in MassSpectrometryReadWriteProcess.

It also includes a set of representation layers for spectra in mzdata::spectrum

Example

use std::fs;
use mzdata::prelude::*;
use mzpeaks::Tolerance;
use mzdata::MZReader;
use mzdata::spectrum::SignalContinuity;

let reader = MZReader::open_path("./test/data/small.mzML").unwrap();
for spectrum in reader {
    println!("Scan {} => BP {}", spectrum.id(), spectrum.peaks().base_peak().mz);

    if spectrum.signal_continuity() == SignalContinuity::Centroid {
        let peak_picked = spectrum.into_centroid().unwrap();
        println!("Matches for 579.155: {:?}",
                 peak_picked.peaks.all_peaks_for(
                    579.155, Tolerance::Da(0.02)
                )
        );
    }
}

It uses mzpeaks to represent peaks and peak lists, and re-exports the basic types. While the high-level types are templated on simple peak types, more complex, application-specific peak types can be substituted. See mzdata::spectrum::bindata for more information about how to directly convert data arrays to peak lists.

Traits

The library makes heavy use of traits to abstract over the implementation details of different file formats. These traits are included in mzdata::prelude. It also imports mzpeaks::prelude.

Re-exports

pub use crate::io::MZReader;

pub use crate::io::MZReaderBuilder;

pub use crate::io::mgf::MGFReader;

pub use crate::io::mgf::MGFWriter;

pub use crate::io::mzml::MzMLReader;

pub use crate::io::mzml::MzMLWriter;

pub use crate::io::mzmlb::MzMLbReader;

pub use crate::io::mzmlb::MzMLbWriter;

pub use crate::io::mzmlb::MzMLbWriterBuilder;

pub use crate::params::Param;

pub use crate::params::ParamList;

pub use crate::spectrum::CentroidSpectrum;

pub use crate::spectrum::RawSpectrum;

pub use crate::spectrum::Spectrum;

pub use mzpeaks;

pub use mzsignal;

Modules

io

Reading and writing mass spectrometry data file formats and abstractions over them.

meta

Metadata describing mass spectrometry data files and their contents.

params

Elements of controlled vocabularies used to describe mass spectra and their components.

prelude

A set of foundational traits used throughout the library.

spectrum

The data structures and components that represent a mass spectrum and how to access their data.

tutorial

A series of written introductions to specific topics in mzdata

utils

Macros

curie

cvmap

delegate_impl_metadata_trait

Delegates the implementation of MSDataFileMetadata to a member. Passing an extra level extended token implements the optional methods.

find_param_method

impl_metadata_trait

Assumes a field for the non-Option facets of the MSDataFileMetadata implementation are present. Passing an extra level extended token implements the optional methods.

impl_param_described

Implement the ParamDescribed trait for type $t, referencing a params member of type Vec<Param>.

impl_param_described_deferred

Implement the ParamDescribed trait for type $t, referencing a params member that is an Option<Vec<Param>> that will lazily be initialized automatically when it is accessed mutably.

mz_read

A macro that dynamically works out how to get a SpectrumSource-derived object from a path or io::Read + io::Seek boxed object. This is meant to be a convenience for working with a scoped file reader without penalty.

mz_write

A macro that dynamically works out how to get a SpectrumWriter from a path or io::Write boxed object.