Fred2.TAPPrediction Module¶
TAPPrediction.PSSM¶
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class
Fred2.TAPPrediction.PSSM.
APSSMTAPPrediction
¶ Bases:
Fred2.Core.Base.ATAPPrediction
Abstract base class for PSSM predictions. Implements predict functionality
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name
¶ The name of the predictor
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predict
(peptides, **kwargs)¶ Returns TAP predictions for given
Peptide
.Parameters: peptides (list( Peptide
) orPeptide
) – A singlePeptide
or a list ofPeptide
Returns: Returns a TAPPredictionResult
object with the prediction resultsReturn type: TAPPredictionResult
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supportedLength
¶ The supported lengths of the predictor
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version
¶ Parameter specifying the version of the prediction method
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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.
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name
¶ The name of the predictor
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predict
(peptides, **kwargs)¶ Returns TAP predictions for given
Peptide
.Parameters: peptides (list( Peptide
) orPeptide
) – A singlePeptide
or a list ofPeptide
Returns: Returns a TAPPredictionResult
object with the prediction resultsReturn type: TAPPredictionResult
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version
¶ The version of the predictor
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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
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name
¶ The name of the predictor
-
predict
(peptides, **kwargs)¶ Returns TAP predictions for given
Peptide
.Parameters: peptides (list( Peptide
) orPeptide
) – A singlePeptide
or a list ofPeptide
Returns: Returns a TAPPredictionResult
object with the prediction resultsReturn type: TAPPredictionResult
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version
¶ The version of the predictor
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TAPPrediction.SVM¶
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class
Fred2.TAPPrediction.SVM.
ASVMTAPPrediction
¶ Bases:
Fred2.Core.Base.ATAPPrediction
,Fred2.Core.Base.ASVM
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encode
(peptides)¶ Returns the feature encoding for peptides
Parameters: peptides (list( Peptide
)/Peptide
) – List of or a singlePeptide
objectReturns: Feature encoding of the Peptide objects Return type: list(Object)
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name
¶ The name of the predictor
-
predict
(peptides, **kwargs)¶ Returns TAP predictions for given
Peptide
.Parameters: peptides (list( Peptide
) orPeptide
) – A singlePeptide
or a list ofPeptide
Returns: Returns a TAPPredictionResult
object with the prediction resultsReturn type: TAPPredictionResult
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supportedLength
¶ The supported lengths of the predictor
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version
¶ Parameter specifying the version of the prediction method
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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
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encode
(peptides)¶ Encodes the
Peptide
with a binary sparse encodingParameters: 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))))
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name
¶ The name of the predictor
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predict
(peptides, **kwargs)¶ Returns predictions for given
Peptide
.Parameters: peptides (list( Peptide
) orPeptide
) – A singlePeptide
or a list ofPeptide
Returns: Returns a TAPPredictionResult
object with the prediction resultsReturn type: TAPPredictionResult
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supportedLength
¶ A list of supported peptide lengths
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version
¶ The version of the predictor
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