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
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distributions
Built Distribution
Hashes for mzml2isa-0.4.22-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4d991e84f2ac1e22c8e5ffaea32b7c82e9b5fa0abe75c05685c16d47c475c502 |
|
MD5 | 0a8a7b9dd182a030c7c82ba60c1bc066 |
|
BLAKE2b-256 | 082c6f12742cb8190572d84098d0229903d397eb915d797b6b60a7308ed29497 |