oktoberfest.pp.convert_raw_to_mzml

oktoberfest.pp.convert_raw_to_mzml(raw_file, output_file, thermo_exe=None)

Convert raw to mzML format.

This function converts RAW files containing spectra from a mass spectrometry run into mzML format. The process makes use of ThermoRawFileParser and requires mono being installed if it is used on MacOS or linux.

Parameters:

• raw_file (Union[str, Path]) – Path to RAW file to be converted to mzML format

• output_file (Union[str, Path]) – Path to the location where the converted spectra should be written to.

• thermo_exe (Union[str, Path, None]) – Path to the executable of ThermoRawFileParser, default depends on the OS: for Windows, it is “ThermoRawFileParser.exe”, while for Linux and MacOS, it is “/opt/compomics/ThermoRawFileParser.exe”.