BasicProteinInferenceAlgorithm#

class pyopenms.BasicProteinInferenceAlgorithm#

Bases: object

Cython implementation of _BasicProteinInferenceAlgorithm

Original C++ documentation is available here: – Inherits from [‘DefaultParamHandler’, ‘ProgressLogger’]

Algorithm class that implements simple protein inference by aggregation of peptide scores.

It has multiple parameter options like the aggregation method, when to distinguish peptidoforms, and if you want to use shared peptides (“use_shared_peptides”). First, the best PSM per spectrum is used, then only the best PSM per peptidoform is aggregated. Peptidoforms can optionally be distinguished via the treat_X_separate parameters: - Modifications (modified sequence string) - Charge states The algorithm assumes posteriors or posterior error probabilities and converts to posteriors initially. Possible aggregation methods that can be set via the parameter “aggregation_method” are: - “best” (default) - “sum” - “product” (ignoring zeroes) Annotation of the number of peptides used for aggregation can be disabled (see parameters). Supports multiple runs but goes through them one by one iterating over the full PeptideIdentification vector. Warning: Does not “link” the peptides to the resulting protein run. If you wish to do that you have to do it manually.

Usage:

__init__(self) → None#

Methods

`__init__`(self)
`endProgress`(self)	Ends the progress display
`getDefaults`(self)	Returns the default parameters
`getLogType`(self)	Returns the type of progress log being used
`getName`(self)	Returns the name
`getParameters`(self)	Returns the parameters
`getSubsections`(self)
`nextProgress`(self)	Increment progress by 1 (according to range begin-end)
`run`	Overload:
`setLogType`(self, in_0)	Sets the progress log that should be used.
`setName`(self, in_0)	Sets the name
`setParameters`(self, param)	Sets the parameters
`setProgress`(self, value)	Sets the current progress
`startProgress`(self, begin, end, label)

endProgress(self) → None#: Ends the progress display

getDefaults(self) → Param#: Returns the default parameters

getLogType(self) → int#: Returns the type of progress log being used

getName(self) → bytes | str | String#: Returns the name

getParameters(self) → Param#: Returns the parameters

getSubsections(self) → List[bytes]#

nextProgress(self) → None#: Increment progress by 1 (according to range begin-end)

run()#

Overload:

run(self, pep_ids: List[PeptideIdentification], prot_ids: List[ProteinIdentification]) → None

Performs basic aggregation-based inference per ProteinIdentification run. See class help.

Parameters:

pep_ids – Vector of peptide identifications
prot_ids – Vector of protein identification runs. Scores will be overwritten and groups added.

Returns:

Writes its results into prot_ids

Overload:

run(self, pep_ids: List[PeptideIdentification], prot_id: ProteinIdentification) → None

Performs basic aggregation-based inference on single ProteinIdentification run. See class help.

Parameters:

pep_ids – Vector of peptide identifications
prot_id – ProteinIdentification run with possible proteins. Scores will be overwritten and groups added.

Returns:

Writes its results into prot_ids

Overload:

run(self, cmap: ConsensusMap, prot_id: ProteinIdentification, include_unassigned: bool) → None

Performs basic aggregation-based inference on identifications in a ConsensusMap. See class help.

prot_id should contain the union of all proteins in the map. E.g. use ConsensusMapMergerAlgorithm and then pass the first=merged run.

Parameters:

cmap – ConsensusMap = Consensus features with metadata and peptide identifications
prot_id – ProteinIdentification run with possible proteins. Scores will be overwritten and groups added.

Returns:

Writes its results into prot_ids

setLogType(self, in_0: int) → None#: Sets the progress log that should be used. The default type is NONE!

setName(self, in_0: bytes | str | String) → None#: Sets the name

setParameters(self, param: Param) → None#: Sets the parameters

setProgress(self, value: int) → None#: Sets the current progress

startProgress(self, begin: int, end: int, label: bytes | str | String) → None#