skip to navigation
skip to content

imzml2isa-qt 0.1.5

A PyQt interface for mzml2isa parser.

Latest Version: 0.1.6


A PyQt interface for mzml2isa parser - imzML edition.


This program is a Graphical User Interface for the
`mzml2isa <https:"" isa-tools="" mzml2isa="">`__ parser. It provides
an easy-to-use interface to convert mzML files to an ISA-Tab Study. It
was made with Python3 and PyQt5.


With PIP

If ``pip`` is present on your system (comes along most of Python install
/ releases), it can be used to install the program and its dependencies:

.. code:: bash

pip3 install imzml2isa-qt

Without PIP

Once dependencies installed, clone the **imzml2isa-qt** repository to a
folder with writing permissions:

.. code:: bash

git clone git://

After that, either run the GUI directly:

.. code:: bash


Or install it locally to run with ``imzmlisa-qt`` command:

.. code:: bash

cd imzml2isa-qt && python3 install


Open the GUI with the ``imzml2isa-qt`` command. To simply parse **.imzML**
files to **ISA**, select the directory containing your files. With
default settings, the program will create the new ISA files in that
folder, assuming the folder's name is the study identifier (*MTBSLxxx*
for instance for MetaboLights studies). This can be changed by unticking
the ``Export result to directory of each study`` box. Once parameters
are set up, click the ``Convert`` button to start the parser.


Generating a study to upload on MetaboLights requires pieces of
information the parser cannot guess from the mzML file alone. To provide
more metadata to your final ISA-Tab files, use the ``Add Metadata``
button to open a new window and update details about your study. Still,
even with all the required fields filled, **the generated ISA needs to
be enhanced after the end of the parsing** (using for instance
`Metabolight pre-packaged ISA
Creator <http:"" metabolights=""/>`__ to add missing fields).

Missing information required for MetaboLights upload are at the moment:
- Study Factors (sample dependent, must be added to the *study* file
and to the *investigation* file)
- Metabolite Assignment Files
- Study Designs


- Either add a ``metabolite assignment file`` field to main window or
change the **mzml2isa** parser behaviour so that it successfully
detects metabolite assignment files and add them to the study file.


File Type Py Version Uploaded on Size
imzml2isa-qt-0.1.5.tar.gz (md5) Source 2017-01-12 600KB
imzml2isa_qt-0.1.5-py3-none-any.whl (md5) Python Wheel 3.5 2017-01-12 647KB