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
CLI
The parser comes with a simple one-liner:
mzml2isa -i /path/to/nmrml_files/ -o /path/to/out_folder -s name_of_studyModule
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 metadataOr 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)1 maintainer
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