pymzml

library2.6.0pypypi✓ verified 86d ago

High-throughput mzML file parsing for mass spectrometry data. Current version 2.6.0, compatible with Python >=3.7. Released irregularly; last stable release Oct 2024.

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pip install pymzml

github ↗homepage ↗

INSTALL

IMPORT

SIG · PYMZML

pymzml

analyticspythonv2.6.0

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

run

✓ from pymzml import run

✗ import pymzml

pymzml is not a module with attributes; use 'from pymzml import run' to get the reader.

Read an mzML file and iterate over spectra. Replace the URL with a local path.

from pymzml import run example_file = 'https://github.com/pymzml/pymzML/raw/main/tests/testdata/example.mzML' reader = run.Reader(example_file) for spectrum in reader: print(spectrum['id'], spectrum['m/z array'].shape)

Debug

Known issues

breakingpymzML 2.x changed the Reader API: 'run.Reader' replaces 'MzMLReader'. Old code using 'from pymzml import MzMLReader' will fail.

fix

Use 'from pymzml import run; reader = run.Reader(file)' instead.

affects: >=2.0.0

deprecatedThe 'get_spectrum' method is deprecated; use iteration over the Reader or indexing with spectrum IDs.

fix

Replace 'reader.get_spectrum(id)' with 'reader[id]' or loop over 'reader'.

affects: >=2.5.0

gotchaFile paths must be either local files or valid URLs. Relative paths may not resolve correctly; use absolute paths or os.path.abspath().

fix

Pass an absolute path or a proper URL.

affects: all

Errors

Common errors & fixes

AttributeError: module 'pymzml' has no attribute 'run'

Importing pymzml directly; run is a submodule not imported by default.

fix

Use: from pymzml import run

ValueError: File not found: ...

The file path is relative and Python's working directory does not match.

fix

Provide an absolute path or download the file and pass the absolute path.

Upgrade

Version history

2.6.0latest on PyPI · released Dec 10, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

25 hits · last 30 days

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Resources

githubhttps://pymzml.github.com ↗

homepagehttps://pymzml.github.com ↗