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) → Union[bytes, str, String]

Return the version of the schema

initializeLookup(self, lookup: SpectrumMetaDataLookup, experiment: MSExperiment, scan_regex: Union[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: Union[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