IDMapper#
- class pyopenms.IDMapper#
Bases:
object
Cython implementation of _IDMapper
- Original C++ documentation is available here
– Inherits from [‘DefaultParamHandler’]
- __init__()#
Overload:
- __init__(self) None
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications
Overload:
- __init__(self, in_0: IDMapper) None
Methods
Overload:
Overload:
getDefaults
(self)Returns the default parameters
getName
(self)Returns the name
getParameters
(self)Returns the parameters
getSubsections
(self)mapPrecursorsToIdentifications
(self, ...)Mapping of peptide identifications to spectra
setName
(self, in_0)Sets the name
setParameters
(self, param)Sets the parameters
- annotate()#
Overload:
- annotate(self, map_: MSExperiment, ids: List[PeptideIdentification], protein_ids: List[ProteinIdentification], clear_ids: bool, mapMS1: bool) None
Mapping method for peak maps
The identifications stored in a PeptideIdentification instance can be added to the corresponding spectrum Note that a PeptideIdentication is added to ALL spectra which are within the allowed RT and MZ boundaries
- Parameters:
map – MSExperiment to receive the identifications
peptide_ids – PeptideIdentification for the MSExperiment
protein_ids – ProteinIdentification for the MSExperiment
clear_ids – Reset peptide and protein identifications of each scan before annotating
map_ms1 – Attach Ids to MS1 spectra using RT mapping only (without precursor, without m/z)
- Raises:
Exception: MissingInformation is thrown if entries of ‘peptide_ids’ do not contain ‘MZ’ and ‘RT’ information
Overload:
- annotate(self, map_: MSExperiment, fmap: FeatureMap, clear_ids: bool, mapMS1: bool) None
Mapping method for peak maps
Add peptide identifications stored in a feature map to their corresponding spectrum This function converts the feature map to a vector of peptide identifications (all peptide IDs from each feature are taken) and calls the respective annotate() function RT and m/z are taken from the peptides, or (if missing) from the feature itself
- Parameters:
map – MSExperiment to receive the identifications
fmap – FeatureMap with PeptideIdentifications for the MSExperiment
clear_ids – Reset peptide and protein identifications of each scan before annotating
map_ms1 – Attach Ids to MS1 spectra using RT mapping only (without precursor, without m/z)
Overload:
- annotate(self, map_: FeatureMap, ids: List[PeptideIdentification], protein_ids: List[ProteinIdentification], use_centroid_rt: bool, use_centroid_mz: bool, spectra: MSExperiment) None
Mapping method for peak maps
If all features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls by default. If not, the positions of the feature centroids are used. The respective coordinates of the centroids are also used for matching (in place of the corresponding ranges from the bounding boxes) if ‘use_centroid_rt’ or ‘use_centroid_mz’ are true
In any case, tolerance in RT and m/z dimension is applied according to the global parameters ‘rt_tolerance’ and ‘mz_tolerance’. Tolerance is understood as “plus or minus x”, so the matching range is actually increased by twice the tolerance value
If several features (incl. tolerance) overlap the position of a peptide identification, the identification is annotated to all of them
- Parameters:
map – MSExperiment to receive the identifications
ids – PeptideIdentification for the MSExperiment
protein_ids – ProteinIdentification for the MSExperiment
use_centroid_rt – Whether to use the RT value of feature centroids even if convex hulls are present
use_centroid_mz – Whether to use the m/z value of feature centroids even if convex hulls are present
spectra – Whether precursors not contained in the identifications are annotated with an empty PeptideIdentification object containing the scan index
- Raises:
Exception: MissingInformation is thrown if entries of ‘ids’ do not contain ‘MZ’ and ‘RT’ information
Overload:
- annotate(self, map_: ConsensusMap, ids: List[PeptideIdentification], protein_ids: List[ProteinIdentification], measure_from_subelements: bool, annotate_ids_with_subelements: bool, spectra: MSExperiment) None
Mapping method for peak maps
If all features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls by default. If not, the positions of the feature centroids are used. The respective coordinates of the centroids are also used for matching (in place of the corresponding ranges from the bounding boxes) if ‘use_centroid_rt’ or ‘use_centroid_mz’ are true
In any case, tolerance in RT and m/z dimension is applied according to the global parameters ‘rt_tolerance’ and ‘mz_tolerance’. Tolerance is understood as “plus or minus x”, so the matching range is actually increased by twice the tolerance value
If several features (incl. tolerance) overlap the position of a peptide identification, the identification is annotated to all of them
- Parameters:
map – MSExperiment to receive the identifications
ids – PeptideIdentification for the MSExperiment
protein_ids – ProteinIdentification for the MSExperiment
measure_from_subelements – Boolean operator set to true if distance estimate from FeatureHandles instead of Centroid
annotate_ids_with_subelements – Boolean operator set to true if store map index of FeatureHandle in peptide identification
spectra – Whether precursors not contained in the identifications are annotated with an empty PeptideIdentification object containing the scan index
- Raises:
Exception: MissingInformation is thrown if entries of ‘ids’ do not contain ‘MZ’ and ‘RT’ information
- getSubsections(self) List[bytes] #
- mapPrecursorsToIdentifications(self, spectra: MSExperiment, ids: List[PeptideIdentification], mz_tol: float, rt_tol: float) IDMapper_SpectraIdentificationState #
Mapping of peptide identifications to spectra
This helper function partitions all spectra into those that had: - no precursor (e.g. MS1 spectra), - at least one identified precursor, - or only unidentified precursor
- Parameters:
spectra – The mass spectra
ids – The peptide identifications
mz_tol – Tolerance used to map to precursor m/z
rt_tol – Tolerance used to map to spectrum retention time
- Returns:
A struct of vectors holding spectra indices of the partitioning