Fred2.CleavagePrediction Module¶

CleavagePrediction.External¶

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.

cleavagePos¶: Parameter specifying the position of aa (within the prediction window) after which the sequence is cleaved (starting from 1)

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 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

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

predict(aa_seq, command=None, options=None, **kwargs)¶

Overwrites ACleavageSitePrediction.predict

Parameters:	aa_seq (list(`Peptide`/`Protein`) or `Peptide`/`Protein`) – A list of or a single `Peptide` or `Protein` object command (str) – The path to a alternative binary (can be used if binary is not globally executable) options (str) – A string of additional options directly past to the external tool
Returns:	A `CleavageSitePredictionResult` object
Return type:	`CleavageSitePredictionResult`

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

supportedLength¶: The supported lengths of the predictor

version¶: Parameter specifying the version of the prediction method

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.

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

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))

predict(aa_seq, command=None, options=None, **kwargs)¶

Overwrites ACleavageSitePrediction.predict

Parameters:	aa_seq (list(`Peptide`/`Protein`) or `Peptide`/`Protein`) – A list of or a single `Peptide` or `Protein` object command (str) – The path to a alternative binary (can be used if binary is not globally executable) options (str) – A string of additional options directly past to the external tool
Returns:	A `CleavageSitePredictionResult` object
Return type:	`CleavageSitePredictionResult`

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

supportedLength¶: The supported lengths of the predictor

version¶: The version of the Method

CleavagePrediction.PSSM¶

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

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`) or `Peptide`) – A list of peptide objects or a single peptide object
Returns:	Returns a `Fred2.Core.Result.CleavageFragmentPredictionResult` object
Return type:	`Fred2.Core.Result.CleavageFragmentPredictionResult`

supportedLength¶: The supported lengths of the predictor

trailingN¶: The number of trailing residues at the N-terminal of the peptide used for prediction

tralingC¶: The number of trailing residues at the C-terminal of the peptide used for prediction

version¶: Parameter specifying the version of the prediction method

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.

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:	aa_seq (list(`Peptide` or `Protein`) or `Peptide`/`Protein`) – A single `Peptide` or ~Fred2.Core.Protein.Protein or a list of `Peptide` or `Protein` length (int) – The peptide length of the cleavage site model. If None the default value is used.
Returns:	Returns a `CleavageSitePredictionResult` object
Return type:	`CleavageSitePredictionResult`

supportedLength¶: The supported lengths of the predictor

version¶: Parameter specifying the version of the prediction method

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.

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:	aa_seq (list(`Peptide` or `Protein`) or `Peptide`/`Protein`) – A single `Peptide`/~Fred2.Core.Protein.Protein or a list of `Peptide`/`Protein` length (int) – The peptide length of the cleavage site model. If None the default value is used.
Returns:	Returns a `CleavageSitePredictionResult` object
Return type:	`CleavageSitePredictionResult`

supportedLength¶: A list of supported peptide lengths

version¶: The version of the predictor

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

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`) or `Peptide`) – A list of peptide objects or a single peptide object
Returns:	Returns a `Fred2.Core.Result.CleavageFragmentPredictionResult` object
Return type:	`Fred2.Core.Result.CleavageFragmentPredictionResult`

supportedLength¶: A list of supported peptide lengths

trailingN¶: The number of trailing residues at the N-terminal of the peptide used for prediction

tralingC¶: The number of trailing residues at the C-terminal of the peptide used for prediction

version¶: The version of the predictor

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:	aa_seq (list(`Peptide` or `Protein`) or `Peptide`/`Protein`) – A single `Peptide`/~Fred2.Core.Protein.Protein or a list of `Peptide`/`Protein` length (int) – The peptide length of the cleavage site model. If None the default value is used.
Returns:	Returns a `CleavageSitePredictionResult` object
Return type:	`CleavageSitePredictionResult`

supportedLength¶: A list of supported peptide lengths

version¶: The version of the predictor

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:	aa_seq (list(`Peptide` or `Protein`) or `Peptide`/`Protein`) – A single `Peptide`/~Fred2.Core.Protein.Protein or a list of `Peptide`/`Protein` length (int) – The peptide length of the cleavage site model. If None the default value is used.
Returns:	Returns a `CleavageSitePredictionResult` object
Return type:	`CleavageSitePredictionResult`

supportedLength¶: A list of supported peptide lengths

version¶: The version of the predictor

Module contents¶

class Fred2.CleavagePrediction.CleavageFragmentPredictorFactory¶

Bases: object

static available_methods()¶

Returns a list of available cleavage site predictors

Returns:	dict(str,list(str)) - dict of cleavage site predictor represented as string and the supported versions

class Fred2.CleavagePrediction.CleavageSitePredictorFactory¶

Bases: object

static available_methods()¶

Returns a list of available cleavage site predictors

Returns:	dict(str,list(int)) - dict of cleavage site predictor represented as string and the supported versions