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mzML file parser and converter to ISA-Tab

Project description

Extract metadata from mzML and imzML files and write them to an ISA-Tab document.

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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)

Features:
  • Extract meta information from mzML files and stores it as a Python dictionary or serialize it into a JSON formatted document.
  • Create 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 or an XLS file.

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 details


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