FeatureFinderIdentificationAlgorithm

class pyopenms.FeatureFinderIdentificationAlgorithm

Bases: object

Cython implementation of _FeatureFinderIdentificationAlgorithm

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1FeatureFinderIdentificationAlgorithm.html

– Inherits from [‘DefaultParamHandler’]

External IDs (peptides_ext, proteins_ext) may be empty, in which case no machine learning or FDR estimation will be performed. Optional seeds from e.g. untargeted FeatureFinders can be added with seeds. Results will be written to features . Caution: peptide IDs will be shrunk to best hit, FFid metavalues added and potential seed IDs added. —– Usage:

from pyopenms import * from urllib.request import urlretrieve urlretrieve(”https://raw.githubusercontent.com/OpenMS/OpenMS/develop/src/tests/topp/FeatureFinderIdentification_1_input.mzML”, “FeatureFinderIdentification_1_input.mzML”) urlretrieve(”https://raw.githubusercontent.com/OpenMS/OpenMS/develop/src/tests/topp/FeatureFinderIdentification_1_input.idXML”, “FeatureFinderIdentification_1_input.idXML”) # ffid_algo = FeatureFinderIdentificationAlgorithm() # load ms data from mzML mzml = MzMLFile() mzml_options = mzml.getOptions() mzml_options.addMSLevel(1) # only MS1 mzml.setOptions(mzml_options) # exp = MSExperiment() mzml.load(“FeatureFinderIdentification_1_input.mzML”, exp) ffid_algo.setMSData(exp) # annotate mzML file features = FeatureMap() features.setPrimaryMSRunPath([b”FeatureFinderIdentification_1_input.idXML”], ffid_algo.getMSData()) # peptides = [] proteins = [] peptides_ext = [] proteins_ext = [] IdXMLFile().load(“FeatureFinderIdentification_1_input.idXML”, proteins, peptides) # #”internal” IDs: ffid_algo.run(peptides, proteins, peptides_ext, proteins_ext, features) # # Terminal output: # Summary statistics (counting distinct peptides including PTMs): # 22 peptides identified (22 internal, 0 additional external) # 16 peptides with features (16 internal, 0 external) # 6 peptides without features (6 internal, 0 external)

__init__()

Cython signature: void FeatureFinderIdentificationAlgorithm()

Methods

__init__	Cython signature: void FeatureFinderIdentificationAlgorithm()
getChromatograms	Cython signature: MSExperiment getChromatograms() Returns chromatogram data as MSExperiment
getDefaults	Cython signature: Param getDefaults() Returns the default parameters
getLibrary	Cython signature: TargetedExperiment getLibrary() Returns constructed assay library
getMSData	Cython signature: MSExperiment getMSData() Returns ms data as MSExperiment
getName	Cython signature: String getName() Returns the name
getParameters	Cython signature: Param getParameters() Returns the parameters
getSubsections	Cython signature: libcpp_vector[String] getSubsections()
run	Cython signature: void run(libcpp_vector[PeptideIdentification] peptides, libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] peptides_ext, libcpp_vector[ProteinIdentification] proteins_ext, FeatureMap & features)
runOnCandidates	Cython signature: void runOnCandidates(FeatureMap & features) Run feature detection on identified features (e.g.
setMSData	Cython signature: void setMSData(const MSExperiment &) Sets ms data
setName	Cython signature: void setName(const String &) Sets the name
setParameters	Cython signature: void setParameters(Param & param) Sets the parameters

getChromatograms()

Cython signature: MSExperiment getChromatograms() Returns chromatogram data as MSExperiment

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getLibrary()

Cython signature: TargetedExperiment getLibrary() Returns constructed assay library

getMSData()

Cython signature: MSExperiment getMSData() Returns ms data as MSExperiment

getName()

Cython signature: String getName() Returns the name

getParameters()

Cython signature: Param getParameters() Returns the parameters

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

run()

• Cython signature: void run(libcpp_vector[PeptideIdentification] peptides, libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] peptides_ext, libcpp_vector[ProteinIdentification] proteins_ext, FeatureMap & features)

Run feature detection :param peptides: Vector of identified peptides :param proteins: Vector of identified proteins :param peptides_ext: Vector of external identified peptides, can be used to transfer ids from other runs :param proteins_ext: Vector of external identified proteins, can be used to transfer ids from other runs :param features: Feature detection results will be added here

• Cython signature: void run(libcpp_vector[PeptideIdentification] peptides, libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] peptides_ext, libcpp_vector[ProteinIdentification] proteins_ext, FeatureMap & features, FeatureMap & seeds)

Run feature detection :param peptides: Vector of identified peptides :param proteins: Vector of identified proteins :param peptides_ext: Vector of external identified peptides, can be used to transfer ids from other runs :param proteins_ext: Vector of external identified proteins, can be used to transfer ids from other runs :param features: Feature detection results will be added here :param seeds: Optional seeds for feature detection from e.g. untargeted FeatureFinders

• Cython signature: void run(libcpp_vector[PeptideIdentification] peptides, libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] peptides_ext, libcpp_vector[ProteinIdentification] proteins_ext, FeatureMap & features, FeatureMap & seeds, String & spectra_file)

Run feature detection :param peptides: Vector of identified peptides :param proteins: Vector of identified proteins :param peptides_ext: Vector of external identified peptides, can be used to transfer ids from other runs :param proteins_ext: Vector of external identified proteins, can be used to transfer ids from other runs :param features: Feature detection results will be added here :param seeds: Optional seeds for feature detection from e.g. untargeted FeatureFinders :param spectra_file: Path will be stored in features in case the MSExperiment has no proper primaryMSRunPath

runOnCandidates()

Cython signature: void runOnCandidates(FeatureMap & features) Run feature detection on identified features (e.g. loaded from an IdXML file)

setMSData()

Cython signature: void setMSData(const MSExperiment &) Sets ms data

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters