PercolatorFeatureSetHelper

class pyopenms.PercolatorFeatureSetHelper

Bases: object

Cython implementation of _PercolatorFeatureSetHelper

Original C++ documentation is available here

Percolator feature set and integration helper

This class contains functions to handle (compute, aggregate, integrate) Percolator features. This includes the calculation or extraction of Percolator features depending on the search engine(s) for later use with PercolatorAdapter. It also includes handling the reintegration of the percolator result into the set of Identifications

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: PercolatorFeatureSetHelper) → None

Methods

__init__

Overload:

addCOMETFeatures(self, peptide_ids, feature_set)

Creates and adds Comet specific Percolator features and registers them in feature_set

addCONCATSEFeatures(self, peptide_id_list, ...)

Adds multiple search engine specific Percolator features and registers them in feature_set

addMASCOTFeatures(self, peptide_ids, feature_set)

Creates and adds Mascot specific Percolator features and registers them in feature_set

addMSGFFeatures(self, peptide_ids, feature_set)

Creates and adds MSGF+ specific Percolator features and registers them in feature_set.

addMULTISEFeatures(self, peptide_ids, ...)

Adds multiple search engine specific Percolator features and registers them in feature_set

addXTANDEMFeatures(self, peptide_ids, ...)

Creates and adds X!Tandem specific Percolator features and registers them in feature_set

checkExtraFeatures(self, psms, extra_features)

Checks and removes requested extra Percolator features that are actually unavailable (to compute)

concatMULTISEPeptideIds(self, ...)

Appends a vector of PeptideIdentification to another and prepares Percolator features in MetaInfo (With the respective key "CONCAT:" + search_engine)

mergeMULTISEPeptideIds(self, ...)

Merges a vector of PeptideIdentification into another and prepares the merged MetaInfo and scores for collection in addMULTISEFeatures for feature registration

mergeMULTISEProteinIds(self, ...)

Concatenates SearchParameter of multiple search engine runs and merges PeptideEvidences, collects used search engines in MetaInfo for collection in addMULTISEFeatures for feature registration
addCOMETFeatures(self, peptide_ids: List[PeptideIdentification], feature_set: List[bytes]) → None

Creates and adds Comet specific Percolator features and registers them in feature_set

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • feature_set – Register of added features

addCONCATSEFeatures(self, peptide_id_list: List[PeptideIdentification], search_engines_used: List[bytes], feature_set: List[bytes]) → None

Adds multiple search engine specific Percolator features and registers them in feature_set

This struct can be used to store both peak or feature indices

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • search_engines_used – The list of search engines to be considered

  • feature_set – Register of added features

addMASCOTFeatures(self, peptide_ids: List[PeptideIdentification], feature_set: List[bytes]) → None

Creates and adds Mascot specific Percolator features and registers them in feature_set

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • feature_set – Register of added features

addMSGFFeatures(self, peptide_ids: List[PeptideIdentification], feature_set: List[bytes]) → None

Creates and adds MSGF+ specific Percolator features and registers them in feature_set. MSGF+ should be run with the addFeatures flag enabled

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • feature_set – Register of added features

addMULTISEFeatures(self, peptide_ids: List[PeptideIdentification], search_engines_used: List[bytes], feature_set: List[bytes], complete_only: bool, limits_imputation: bool) → None

Adds multiple search engine specific Percolator features and registers them in feature_set

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • search_engines_used – The list of search engines to be considered

  • feature_set – Register of added features

  • complete_only – Will only add features for PeptideIdentifications where all given search engines identified something

  • limits_imputation – Uses C++ numeric limits as imputed values instead of min/max of that feature

addXTANDEMFeatures(self, peptide_ids: List[PeptideIdentification], feature_set: List[bytes]) → None

Creates and adds X!Tandem specific Percolator features and registers them in feature_set

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • feature_set – Register of added features

checkExtraFeatures(self, psms: List[PeptideHit], extra_features: List[bytes]) → None

Checks and removes requested extra Percolator features that are actually unavailable (to compute)

Parameters

  • psms – The vector of PeptideHit to be checked

  • extra_features – The list of requested extra features

concatMULTISEPeptideIds(self, all_peptide_ids: List[PeptideIdentification], new_peptide_ids: List[PeptideIdentification], search_engine: Union[bytes, str, String]) → None

Appends a vector of PeptideIdentification to another and prepares Percolator features in MetaInfo (With the respective key “CONCAT:” + search_engine)

Parameters

  • all_peptide_ids – PeptideIdentification vector to append to

  • new_peptide_ids – PeptideIdentification vector to be appended

  • search_engine – Search engine to depend on for feature creation

mergeMULTISEPeptideIds(self, all_peptide_ids: List[PeptideIdentification], new_peptide_ids: List[PeptideIdentification], search_engine: Union[bytes, str, String]) → None

Merges a vector of PeptideIdentification into another and prepares the merged MetaInfo and scores for collection in addMULTISEFeatures for feature registration

Parameters

  • all_peptide_idsL – PeptideIdentification vector to be merged into

  • new_peptide_idsL – PeptideIdentification vector to merge

  • search_engineL – Search engine to create features from their scores

mergeMULTISEProteinIds(self, all_protein_ids: List[ProteinIdentification], new_protein_ids: List[ProteinIdentification]) → None

Concatenates SearchParameter of multiple search engine runs and merges PeptideEvidences, collects used search engines in MetaInfo for collection in addMULTISEFeatures for feature registration

Parameters

  • all_protein_ids – ProteinIdentification vector to be merged into

  • new_protein_ids – ProteinIdentification vector to merge