XQuestResultXMLFile#

class pyopenms.XQuestResultXMLFile#

Bases: object

Cython implementation of _XQuestResultXMLFile

__init__()#

Overload:

Overload:

Methods

`__init__`	Overload:
`getMaxScore`(self)	Returns maximum score among the hits in the file
`getMinScore`(self)	Returns minimum score among the hits in the file
`getNumberOfHits`(self)	Returns the total number of hits in the file
`getVersion`(self)	Return the version of the schema
`load`(self, filename, pep_ids, prot_ids)	Load the content of the xquest.xml file into the provided data structures
`store`(self, filename, poid, peid)	Stores the identifications in a xQuest XML file
`writeXQuestXMLSpec`	Overload:

getMaxScore(self) → float#: Returns maximum score among the hits in the file

getMinScore(self) → float#: Returns minimum score among the hits in the file

getNumberOfHits(self) → int#: Returns the total number of hits in the file

getVersion(self) → bytes | str | String#: Return the version of the schema

load(self, filename: bytes | str | String, pep_ids: List[PeptideIdentification], prot_ids: List[ProteinIdentification]) → None#

Load the content of the xquest.xml file into the provided data structures

Parameters:

filename – Filename of the file which is to be loaded
pep_ids – Where the spectra with identifications of the input file will be loaded to
prot_ids – Where the protein identification of the input file will be loaded to

store(self, filename: bytes | str | String, poid: List[ProteinIdentification], peid: List[PeptideIdentification]) → None#: Stores the identifications in a xQuest XML file

writeXQuestXMLSpec()#

Overload:

writeXQuestXMLSpec(self, out_file: bytes | str | String, base_name: bytes | str | String, preprocessed_pair_spectra: OPXL_PreprocessedPairSpectra, spectrum_pairs: List[List[int, int]], all_top_csms: List[List[CrossLinkSpectrumMatch]], spectra: MSExperiment, test_mode: bool) → None

Writes spec.xml output containing matching peaks between heavy and light spectra after comparing and filtering

Parameters:

out_file – Path and filename for the output file
base_name – The base_name should be the name of the input spectra file without the file ending. Used as part of an identifier string for the spectra
preprocessed_pair_spectra – The preprocessed spectra after comparing and filtering
spectrum_pairs – Indices of spectrum pairs in the input map
all_top_csms – CrossLinkSpectrumMatches, from which the IDs were generated. Only spectra with matches are written out
spectra – The spectra, that were searched as a PeakMap. The indices in spectrum_pairs correspond to spectra in this map

Overload:

writeXQuestXMLSpec(self, out_file: bytes | str | String, base_name: bytes | str | String, all_top_csms: List[List[CrossLinkSpectrumMatch]], spectra: MSExperiment, test_mode: bool) → None

Writes spec.xml output containing spectra for visualization. This version of the function is meant to be used for label-free linkers

Parameters:

out_file – Path and filename for the output file
base_name – The base_name should be the name of the input spectra file without the file ending. Used as part of an identifier string for the spectra
all_top_csms – CrossLinkSpectrumMatches, from which the IDs were generated. Only spectra with matches are written out
spectra – The spectra, that were searched as a PeakMap