Fred2.CleavagePrediction Module¶
CleavagePrediction.External¶
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class
Fred2.CleavagePrediction.External.
AExternalCleavageSitePrediction
¶ Bases:
Fred2.Core.Base.ACleavageSitePrediction
,Fred2.Core.Base.AExternal
Abstract base class for external cleavage site prediction methods. Implements predict functionality.
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cleavagePos
¶ Parameter specifying the position of aa (within the prediction window) after which the sequence is cleaved (starting from 1)
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command
¶ Defines the commandline call for external tool
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get_external_version
(path=None)¶ Returns the external version of the tool by executing >{command} –version
might be dependent on the method and has to be overwritten therefore it is declared abstract to enforce the user to overwrite the method. The function in the base class can be called with super()
Parameters: path (str) – - Optional specification of executable path if deviant from self.__command
Returns: The external version of the tool or None if tool does not support versioning Return type: str
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is_in_path
()¶ Checks whether the specified execution command can be found in PATH
Returns: Whether or not command could be found in PATH Return type: bool
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name
¶ The name of the predictor
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parse_external_result
(file)¶ Parses external results and returns the result
Parameters: file (str) – The file path or the external prediction results Returns: A dictionary containing the prediction results Return type: dict
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predict
(aa_seq, command=None, options=None, **kwargs)¶ Overwrites ACleavageSitePrediction.predict
Parameters: Returns: A
CleavageSitePredictionResult
objectReturn type: CleavageSitePredictionResult
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prepare_input
(input, file)¶ Prepares the data :attr:_input and writes them to :attr:_file in the special format used by the external tool
Parameters: - input (list(str)) – The input data (here peptide sequences)
- file (File) – A file handler with which the data are written to file
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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.CleavagePrediction.External.
NetChop_3_1
¶ Bases:
Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction
,Fred2.Core.Base.AExternal
Implements NetChop Cleavage Site Prediction (v. 3.1).
Note
Nielsen, M., Lundegaard, C., Lund, O., & Kesmir, C. (2005). The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics, 57(1-2), 33-41.
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cleavagePos
¶ Parameter specifying the position of aa (within the prediction window) after which the sequence is cleaved
-
command
¶ Defines the commandline call for external tool
-
get_external_version
(path=None)¶ Returns the external version of the tool by executing >{command} –version
might be dependent on the method and has to be overwritten therefore it is declared abstract to enforce the user to overwrite the method. The function in the base class can be called with super()
Parameters: path (str) – - Optional specification of executable path if deviant from :attr:self.__command
Returns: The external version of the tool or None if tool does not support versioning Return type: str
-
is_in_path
()¶ Checks whether the specified execution command can be found in PATH
Returns: Whether or not command could be found in PATH Return type: bool
-
name
¶ The name of the predictor
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parse_external_result
(file, hash_dict)¶ Parses external results and returns the result
Parameters: - file (str) – The file path or the external prediction results
- hash_dict (dict(int,Protein)) – A hash dict mapping from internal ID to Protein object du to ID length restriction of NetChop
Returns: Returns a dictionary with the prediction results
Return type: dict(str,dict((str,int),float))
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predict
(aa_seq, command=None, options=None, **kwargs)¶ Overwrites ACleavageSitePrediction.predict
Parameters: Returns: A
CleavageSitePredictionResult
objectReturn type: CleavageSitePredictionResult
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prepare_input
(input, file)¶ Prepares the data and writes them to _file in the special format used by the external tool
Parameters: - input (dict(int,Protein/Peptide)) – The input data (here peptide sequences)
- file (File) – A file handler with which the data are written to file
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supportedLength
¶ The supported lengths of the predictor
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version
¶ The version of the Method
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CleavagePrediction.PSSM¶
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class
Fred2.CleavagePrediction.PSSM.
APSSMCleavageFragmentPredictor
¶ Bases:
Fred2.Core.Base.ACleavageFragmentPrediction
Abstract base class for PSSM predictions.
This implementation only supports cleavage fragment prediction not site prediction
Implements predict functionality
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cleavagePos
¶ Parameter specifying the position of aa (within the prediction window) after which the sequence is cleaved
-
name
¶ The name of the predictor
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predict
(peptides, **kwargs)¶ Takes peptides plus their trailing C and N-terminal residues to predict the probability that this n-mer was produced by proteasomal cleavage. It returns the score and the peptide sequence in a AResult object. Row-IDs are the peitopes column is the prediction score.
Parameters: peptides (list( Peptide
) orPeptide
) – A list of peptide objects or a single peptide objectReturns: Returns a Fred2.Core.Result.CleavageFragmentPredictionResult
objectReturn type: Fred2.Core.Result.CleavageFragmentPredictionResult
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supportedLength
¶ The supported lengths of the predictor
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trailingN
¶ The number of trailing residues at the N-terminal of the peptide used for prediction
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tralingC
¶ The number of trailing residues at the C-terminal of the peptide used for prediction
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version
¶ Parameter specifying the version of the prediction method
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class
Fred2.CleavagePrediction.PSSM.
APSSMCleavageSitePredictor
¶ Bases:
Fred2.Core.Base.ACleavageSitePrediction
Abstract base class for PSSM predictions. This implementation only supports cleavage site prediction not fragment prediction. Implements predict functionality.
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cleavagePos
¶ Parameter specifying the position of aa (within the prediction window) after which the sequence is cleaved (starting from 1)
-
name
¶ The name of the predictor
-
predict
(aa_seq, length=None, **kwargs)¶ Returns predictions for given peptides.
Parameters: Returns: Returns a
CleavageSitePredictionResult
objectReturn type:
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supportedLength
¶ The supported lengths of the predictor
-
version
¶ Parameter specifying the version of the prediction method
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class
Fred2.CleavagePrediction.PSSM.
PCM
¶ Bases:
Fred2.CleavagePrediction.PSSM.APSSMCleavageSitePredictor
Implements the PCM cleavage prediction method.
Note
Doennes, P., and Kohlbacher, O. (2005). Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Science, 14(8), 2132-2140.
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cleavagePos
¶ Parameter specifying the position of aa (within the prediction window) after which the sequence is cleaved
-
name
¶ The name of the predictor
-
predict
(peptides, length=None, **kwargs)¶ Returns predictions for given peptides.
Parameters: Returns: Returns a
CleavageSitePredictionResult
objectReturn type:
-
supportedLength
¶ A list of supported peptide lengths
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version
¶ The version of the predictor
-
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class
Fred2.CleavagePrediction.PSSM.
PSSMGinodi
¶ Bases:
Fred2.CleavagePrediction.PSSM.APSSMCleavageFragmentPredictor
Implements the Cleavage Fragment prediction method of Ginodi et al.
Note
Ido Ginodi, Tal Vider-Shalit, Lea Tsaban, and Yoram Louzoun Precise score for the prediction of peptides cleaved by the proteasome Bioinformatics (2008) 24 (4): 477-483
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cleavagePos
¶ Parameter specifying the position of aa (within the prediction window) after which the sequence is cleaved
-
name
¶ The name of the predictor
-
predict
(peptides, **kwargs)¶ Takes peptides plus their trailing C and N-terminal residues to predict the probability that this n-mer was produced by proteasomal cleavage. It returns the score and the peptide sequence in a AResult object. Row-IDs are the peitopes column is the prediction score.
Parameters: peptides (list( Peptide
) orPeptide
) – A list of peptide objects or a single peptide objectReturns: Returns a Fred2.Core.Result.CleavageFragmentPredictionResult
objectReturn type: Fred2.Core.Result.CleavageFragmentPredictionResult
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supportedLength
¶ A list of supported peptide lengths
-
trailingN
¶ The number of trailing residues at the N-terminal of the peptide used for prediction
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tralingC
¶ The number of trailing residues at the C-terminal of the peptide used for prediction
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version
¶ The version of the predictor
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class
Fred2.CleavagePrediction.PSSM.
ProteaSMMConsecutive
¶ Bases:
Fred2.CleavagePrediction.PSSM.APSSMCleavageSitePredictor
Implements the ProteaSMM cleavage prediction method.
Note
Tenzer, S., et al. “Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding.” Cellular and Molecular Life Sciences CMLS 62.9 (2005): 1025-1037.
This model represents the consecutive proteasom
The matrices are generated not using the preon-dataset since a recent study has show that including those worsened the results.
Note
Calis, Jorg JA, et al. “Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs.” Immunogenetics (2014): 1-9.
-
cleavagePos
¶ Parameter specifying the position of aa (within the prediction window) after which the sequence is cleaved
-
name
¶ The name of the predictor
-
predict
(peptides, length=None, **kwargs)¶ Returns predictions for given peptides.
Parameters: Returns: Returns a
CleavageSitePredictionResult
objectReturn type:
-
supportedLength
¶ A list of supported peptide lengths
-
version
¶ The version of the predictor
-
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class
Fred2.CleavagePrediction.PSSM.
ProteaSMMImmuno
¶ Bases:
Fred2.CleavagePrediction.PSSM.APSSMCleavageSitePredictor
Implements the ProteaSMM cleavage prediction method.
Note
Tenzer, S., et al. “Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding.” Cellular and Molecular Life Sciences CMLS 62.9 (2005): 1025-1037.
This model represents the immuno proteasom
The matrices are generated not using the preon-dataset since a recent study has show that including those worsened the results.
Note
Calis, Jorg JA, et al. “Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs.” Immunogenetics (2014): 1-9.
-
cleavagePos
¶ Parameter specifying the position of aa (within the prediction window) after which the sequence is cleaved
-
name
¶ The name of the predictor
-
predict
(peptides, length=None, **kwargs)¶ Returns predictions for given peptides.
Parameters: Returns: Returns a
CleavageSitePredictionResult
objectReturn type:
-
supportedLength
¶ A list of supported peptide lengths
-
version
¶ The version of the predictor
-