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

__init__	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

getVersion(self) → bytes | str | String

Return the version of the schema

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