`mzml2isa`

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

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 <http://www.ebi.ac.uk/metabolights/>__)

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 <http://2isa.readthedocs.io/en/latest/mzml2isa/install.html> of the online documentation <http://2isa.readthedocs.io/en/latest/mzml2isa/index.html>.

Usage

CLI '''

.. code:: bash

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

Python Module '''''''''''''

See the Usage page <http://2isa.readthedocs.io/en/latest/mzml2isa/usage.html> and the Examples page <http://2isa.readthedocs.io/en/latest/mzml2isa/examples.html> for more information.

Metabolights

To download some real data from MetaboLights <http://www.ebi.ac.uk/metabolights/>__ studies to test the converter with, run

.. code:: bash

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/metabolight\ s folder and then run mzml2isa on those files..

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

.. code:: bash