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mzml2isa - mzML to ISA-tab parsing tool

Project description

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure

Version Py versions Git Build Status License RTD doc

Overview

mzml2isa is a Python3 program that can be used to generate an ISA-Tab structure out of mzML files, providing the backbone of a study which can then be edited with an ISA editing tool (see MetaboLights pre-packaged ISA Creator)

Currently the program does the following:
  • Extract meta information from mzML files and store as either python dictionary or JSON format
  • Create an ISA-Tab file structure with relevant meta information
  • 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 details


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