mzXMLConverter

This repository contains a script for converting mzXML files to a CSV file with only the m/z values and intensity values.

Installation

Create a virtual environment:

python -m venv venv

Install packages:

On Linux / MacOS:

source venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt

On Windows:

venv\Scripts\activate
pip install --upgrade pip
pip install -r requirements.txt

Generating an packaged executable

We generate a console executable version of the script using pyinstaller. Run this command on the type of OS you want to support:

source venv/bin/activate
pyinstaller --console mzxmlconverter.py

or

source venv/bin/activate
pyinstaller --console --onefile mzxmlconverter.py

Then distribute the content from the dist directory.

Usage of the script

Start by downloading the release package for your operating system from Releases. Then unpack it somewhere appropriate on your computer.

For Windows there are two release zip archives: mzxmlconverter.zip the program in a folder together with a lot of necessary extra files. mzxmlconverter_onefile.zip contains one file called mzxmlconverter.exe with everything needed pack into a single file. Both works.

WARNING: On Windows running either package is super slow because of a antimalware scan everytime the program starts.

MacOS

Open a terminal window and start by executing the command

export PATH=$PATH:/your_path_to/mzxmlconverter/

Now you can execute the program in the same terminal window by

mzxmlconverter -i path_to_file.mzXML -o path_to_output_directory

Windows

Open a terminal window and change into the directory where you installed the program

cd your_path_to\mzxmlconverter.exe

Now you can execute the program in the same terminal window by

mzxmlconverter -i path_to_file.mzXML -o path_to_output_directory