nmrml2isa

Parser to get meta information from nmrML file and parse relevant information to an ISA-Tab structure

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)