MascotXMLFile#
- class pyopenms.MascotXMLFile#
Bases:
object
Cython implementation of _MascotXMLFile
- Original C++ documentation is available here
– Inherits from [‘XMLFile’]
- __init__()#
Overload:
- __init__(self) None
Overload:
- __init__(self, in_0: MascotXMLFile) None
Methods
Overload:
getVersion
(self)Return the version of the schema
initializeLookup
(self, lookup, experiment, ...)Initializes a helper object for looking up spectrum meta data (RT, m/z)
load
(self, filename, protein_identification, ...)Loads data from a Mascot XML file
- initializeLookup(self, lookup: SpectrumMetaDataLookup, experiment: MSExperiment, scan_regex: bytes | str | String) None #
Initializes a helper object for looking up spectrum meta data (RT, m/z)
- Parameters:
lookup – Helper object to initialize
experiment – Experiment containing the spectra
scan_regex – Optional regular expression for extracting information from references to spectra
- load(self, filename: bytes | str | String, protein_identification: ProteinIdentification, id_data: List[PeptideIdentification], rt_mapping: SpectrumMetaDataLookup) None #
Loads data from a Mascot XML file
- Parameters:
filename – The file to be loaded
protein_identification – Protein identifications belonging to the whole experiment
id_data – The identifications with m/z and RT
lookup – Helper object for looking up spectrum meta data
- Raises:
Exception: FileNotFound is thrown if the file does not exists
- Raises:
Exception: ParseError is thrown if the file does not suit to the standard