Parser to extract meta information from mzML mass spectrometry files and parse relevant information to a ISA-Tab structure

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Overview

mzml2isa is a Python3 program that can automatically generate ISA-Tab document structure metadata files from raw XML metabolomics data files (mzML open access data format). The mzml2ISA tool provides the backbone of ISA-Tab metabolomics study which can then be edited with an ISA editing tool, ISAcreator (see MetaboLights pre-packaged ISA Creator)

Currently the program does the following:

  • Extract meta information from mzML files and stores it as either python dictionary or JSON format

  • Creates an ISA-Tab file structure with relevant meta information filled in.

  • Add additional metadata that cannot be parsed from mzML files to the ISA-Tab files through a JSON formatted dictionnary.

Install

See the Installation page of the online documentation.

Usage

CLI

mzml2isa -i /path/to/mzml_files/ -o /path/to/out_folder/ -s name_of_study

Python Module

See the Usage page and the Examples page for more information.

Metabolights

To download some real data from MetaboLights studies to test the converter with, run

python scripts/metabolights-dl.py <size>

from inside the repository, where size is the maximum size in GiB you can allocate to download files. The script will download the files to the example_files/metabolights folder and then run mzml2isa on those files..

If you use a *NIX machine with curlftpfs and bash available, you can also run

scripts/metabolights.sh

to mount the database to the example directory and start converting mzML studies.

Workflow

workflow

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (1.1.1)

2 maintainers

PyPI data
Data sourced directly from PyPI's database.
Avatar for althonos from gravatar.com althonos Avatar for tomnl from gravatar.com tomnl

Credits

Author: Thomas Lawson, Martin Larralde

License

GNU General Public License v3 (GPLv3) (GPLv3)

Tags

Metabolomics Mass spectrometry metabolites ISA Tab mzML parsing

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