nmrml2isa 0.3.1

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)