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
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: 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: 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