mzML 2 ISA-Tab

About

Parser to get meta information from mzML file and create an ISA-Tab file structure with the relevant meta information.

Still a few things to complete and the code needs tidying up but the basic functionality is there. Does the following:

• Extract meta information from mzML files and store as either python dictionary or JSON format
• Create an ISA-Tab file structure with relevant meta information
• Can be used as standalone script or python package, see scripts/ for examples

Workflow

Install the python package

git clone https://github.com/Tomnl/mzml2isa.git

cd mzml2isa

# if in Linux
sudo python setup.py install

# if in windows need admin rights
python setup.py install

mzML to ISA-tab parsing

Can use the system command that ships with the library:

mzml2isa -i /path/to/mzml_files/ -o /path/to/out_folder/ -s new_metabolomics_thing

Or you can import the package

from mzml2isa import parsing

in_dir = "/path/to/mzml_files/"
out_dir = "/path/to/out_folder/"
study_identifier_name = "new_metabolomics_thing"

parsing.full_parse(in_dir, out_dir, study_identifier_name)

Meta extraction

If you just want to extract meta information:

from mzml2isa import mzml

onefile = os.path.join(in_dir,"samp1.mzML")
mm = mzml.mzMLmeta(onefile)

# python dictionary format
print mm.meta

# JSON format
print mm.meta_json

Metabolights

To download some real data from MetaboLights studies to test the converter with, run

python scripts/metabolights-dl.py <size>

where size is the maximum size in GiB you can allocate to download files.

If you are on a *NIX machine with curlftpfs installed, you can also run

scripts/metabolights.sh

to mount the database to the example directory and start converting mzML studies.

Todo

• Check to see how compatible with MetaboLights upload

Ref

For ontology extraction i used a modified version from this blog [1], and modified slightly the class from pymzml [2]

[1] http://blog.nextgenetics.net/?e=6

[2] http://pymzml.github.io/