Skip to content

ISA-tools/nmrml2isa

master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

nmrml2isa

Version Py versions Git Build Status License RTD doc DOI

NMRML

Overview

nmrml2isa is a Python3 program that can be used to generate an ISA-Tab structured investigation out of nmrML files, providing the backbone of a study that can then be edited with an ISA editing tool (see MetaboLights pre-packaged ISA Creator)

Install

See the Installation page of the online documentation.

Use

See the Usage page and the Examples page for more detailed descriptions of usage and examples.

CLI

The parser comes with a simple one-liner:

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

Module

It possible to import nmrml2isa as a Python module:

from nmrml2isa import parsing

in_dir = "/path/to/nmrml_files/"
out_dir = "/path/to/out_folder/"
study_identifier_name = "name_of_study"

parsing.full_parse(in_dir, out_dir, study_identifier_name)

Meta extraction

If you just want to extract the meta information without writing them in ISA-Tab files, it is possible to do so either by running the nmrml2isa.nmrml module as main:

python -m nmrml2isa.nmrml /path/to/your/file.nmrML
# this will produce a JSON dict of all extracted metadata

Or within a python program with the nmrml submodule:

from nmrml2isa import nmrml

nmrml_path = "/path/to/file.nmrML"
nmrml_meta = nmrml.nmrMLmeta(nmrml_path)

# python dictionnary
print(nmrml_meta.meta)

# json dictionnary
print(nmrml_meta.meta_json)

About

Generate ISA-Tab studies from .nmrML files

Resources

License

GPL-3.0, GPL-3.0 licenses found

Licenses found

GPL-3.0
LICENSE
GPL-3.0
COPYING

Stars

Watchers

Forks

Packages

No packages published

Languages