Fred2.TAPPrediction Module¶

TAPPrediction.PSSM¶

class Fred2.TAPPrediction.PSSM.APSSMTAPPrediction¶

Bases: Fred2.Core.Base.ATAPPrediction

Abstract base class for PSSM predictions. Implements predict functionality

name¶: The name of the predictor

predict(peptides, **kwargs)¶

Returns TAP predictions for given Peptide.

Parameters:	peptides (list(`Peptide`) or `Peptide`) – A single `Peptide` or a list of `Peptide`
Returns:	Returns a `TAPPredictionResult` object with the prediction results
Return type:	`TAPPredictionResult`

supportedLength¶: The supported lengths of the predictor

version¶: Parameter specifying the version of the prediction method

class Fred2.TAPPrediction.PSSM.SMMTAP¶

Bases: Fred2.TAPPrediction.PSSM.APSSMTAPPrediction

Implementation of SMMTAP.

Note

Peters, B., Bulik, S., Tampe, R., Van Endert, P. M., & Holzhuetter, H. G. (2003). Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. The Journal of Immunology, 171(4), 1741-1749.

name¶: The name of the predictor

predict(peptides, **kwargs)¶

Returns TAP predictions for given Peptide.

Parameters:	peptides (list(`Peptide`) or `Peptide`) – A single `Peptide` or a list of `Peptide`
Returns:	Returns a `TAPPredictionResult` object with the prediction results
Return type:	`TAPPredictionResult`

supportedLength¶: A list of supported Peptide lengths

version¶: The version of the predictor

class Fred2.TAPPrediction.PSSM.TAPDoytchinova¶

Bases: Fred2.TAPPrediction.PSSM.APSSMTAPPrediction

Implements the TAP prediction model from Doytchinova.

Note

Doytchinova, I., Hemsley, S. and Flower, D. R. Transporter associated with antigen processing preselection of peptides binding to the MHC: a bioinformatic evaluation. J. Immunol, 2004, 173, 6813-6819

name¶: The name of the predictor

predict(peptides, **kwargs)¶

Returns TAP predictions for given Peptide.

Parameters:	peptides (list(`Peptide`) or `Peptide`) – A single `Peptide` or a list of `Peptide`
Returns:	Returns a `TAPPredictionResult` object with the prediction results
Return type:	`TAPPredictionResult`

supportedLength¶: A list of supported Peptide lengths

version¶: The version of the predictor

TAPPrediction.SVM¶

class Fred2.TAPPrediction.SVM.ASVMTAPPrediction¶

Bases: Fred2.Core.Base.ATAPPrediction, Fred2.Core.Base.ASVM

encode(peptides)¶

Returns the feature encoding for peptides

Parameters:	peptides (list(`Peptide`)/`Peptide`) – List of or a single `Peptide` object
Returns:	Feature encoding of the Peptide objects
Return type:	list(Object)

name¶: The name of the predictor

predict(peptides, **kwargs)¶

Returns TAP predictions for given Peptide.

Parameters:	peptides (list(`Peptide`) or `Peptide`) – A single `Peptide` or a list of `Peptide`
Returns:	Returns a `TAPPredictionResult` object with the prediction results
Return type:	`TAPPredictionResult`

supportedLength¶: The supported lengths of the predictor

version¶: Parameter specifying the version of the prediction method

class Fred2.TAPPrediction.SVM.SVMTAP¶

Bases: Fred2.TAPPrediction.SVM.ASVMTAPPrediction

Implements SVMTAP prediction of Doeness et al.

Note

Doennes, P. and Kohlbacher, O. Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci, 2005

encode(peptides)¶

Encodes the Peptide with a binary sparse encoding

Parameters:	peptides (list(str)) – A list of `Peptide`
Returns:	Dictionary with `Peptide` as key and feature encoding as value (see svmlight encoding scheme http://svmlight.joachims.org/)
Return type:	dict(`Peptide`, (tuple(int, list(tuple(int,float))))

name¶: The name of the predictor

predict(peptides, **kwargs)¶

Returns predictions for given Peptide.

Parameters:	peptides (list(`Peptide`) or `Peptide`) – A single `Peptide` or a list of `Peptide`
Returns:	Returns a `TAPPredictionResult` object with the prediction results
Return type:	`TAPPredictionResult`

supportedLength¶: A list of supported peptide lengths

version¶: The version of the predictor

Module contents¶

class Fred2.TAPPrediction.TAPPredictorFactory¶

Bases: object

static available_methods()¶

Returns a dictionary of available TAP predictors and the supported versions

Returns:	dict(str, list(str)) - A dictionary of TAP predictors represented as string and supported versions