Examples¶
CLI¶
Create a new MetaboLights study with existing nmrML data:
mzml2isa -i "/home/metabolomics/NMRML study" -o "/home/metabolomics/isa" -s MZML1
This will create a new folder and write the following ISA-Tab files:
/
└ home/
└ metabolomics/
└ isa/
├ a_MZML1_metabolite_profiling_mass_spectrometry.txt
├ i_Investigation.txt
└ s_MZML1.txt
Python module¶
Note
Syntax for imzML and mzML is the same, except when the class mzMLmeta is used: for imzML files, simply replace mzMLmeta with imzMLmeta.
Extract metadata of a file called sample1.mzML and print a JSON dictionary containing those metadata
python -m mzml2isa.mzml sample1.mzML
Or within a Python program
from mzml2isa.mzml import mzMLmeta
mz = mzMLmeta('sample1.mzML')
# json formatted dict
print(mz.meta_json)
# same metadata, Python dict
print(mz.meta['Sample Name']['value'])