Package org.snpeff.spliceSites

Class SpliceTypes

java.lang.Object

org.snpeff.spliceSites.SpliceTypes

public class SpliceTypes
extends java.lang.Object

Analyze sequences from splice sites

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static int	MAX_SPLICE_SIZE
static int	SIZE_BRANCH
static int	THRESHOLD_COUNT
static double	THRESHOLD_ENTROPY
static double	THRESHOLD_P

Constructor Summary

Constructors

Constructor	Description
SpliceTypes(Config config)

Method Summary

Modifier and Type	Method	Description
Tuple<java.lang.Double,java.lang.Integer>	addBestU12Score(Transcript tr, java.lang.String chrSeq, java.lang.String donorAcceptor, int intronStart, int intronEnd)	Calculate the best U12 score.
boolean	analyzeAndCreate()	Analyze and create conserved splice sites donor-acceptor pairs.
Tuple<java.lang.Double,java.lang.Integer>	bestU12Score(java.lang.String seq)	Find the best score for PWM matrix in U12 branch points
double	branchU12Threshold(double thresholdU12Percentile)	Calculate threshold of U12 PWM scores Pick the score that gives a 'thresholdU12Percentile'.
void	createSpliceFasta(java.lang.String outputDir)	Create one fasta file for each donor-acceptor pair
java.lang.String	getAcceptor(int i)
java.lang.String	getAcceptorsByIntron(java.lang.String intronKey)
java.lang.String	getBranchByIntron(java.lang.String intronKey)
java.util.List<SpliceSiteBranchU12>	getBranchU12(java.lang.String donorAcceptor)	Add a SpliceSiteBranchU12 for this donor-Acceptor pair
java.lang.String	getDonor(int i)
int	getDonorAccPairSize()
java.lang.String	getDonorByIntron(java.lang.String intronKey)
java.util.Set<java.lang.String>	getIntronKeySet()
void	setDebug(boolean debug)
void	setGenomeFasta(java.lang.String genomeFasta)
void	setTranscriptSet(TranscriptSet transcriptSet)
void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAX_SPLICE_SIZE

public static int MAX_SPLICE_SIZE

SIZE_BRANCH

public static int SIZE_BRANCH

THRESHOLD_ENTROPY

public static final double THRESHOLD_ENTROPY

See Also:

Constant Field Values

THRESHOLD_COUNT

public static final int THRESHOLD_COUNT

See Also:

Constant Field Values

THRESHOLD_P

public static final double THRESHOLD_P

See Also:

Constant Field Values

Constructor Detail

SpliceTypes

public SpliceTypes(Config config)

Method Detail

addBestU12Score

public Tuple<java.lang.Double,java.lang.Integer> addBestU12Score(Transcript tr,
                                                                       java.lang.String chrSeq,
                                                                       java.lang.String donorAcceptor,
                                                                       int intronStart,
                                                                       int intronEnd)

Calculate the best U12 score. If the score is higher than 'thresholdU12Score' then add the chr:pos data to a list

Returns:

A Tuple having the best score and best position

analyzeAndCreate

public boolean analyzeAndCreate()

Analyze and create conserved splice sites donor-acceptor pairs.

bestU12Score

public Tuple<java.lang.Double,java.lang.Integer> bestU12Score(java.lang.String seq)

Find the best score for PWM matrix in U12 branch points

Parameters:

seq -

Returns:

A Tuple having the best score and best position

branchU12Threshold

public double branchU12Threshold(double thresholdU12Percentile)

Calculate threshold of U12 PWM scores Pick the score that gives a 'thresholdU12Percentile'. E.g. branchU12Threshold(0.95) gives the 95% percentile threshold

createSpliceFasta

public void createSpliceFasta(java.lang.String outputDir)

Create one fasta file for each donor-acceptor pair

getAcceptor

public java.lang.String getAcceptor(int i)

getAcceptorsByIntron

public java.lang.String getAcceptorsByIntron(java.lang.String intronKey)

getBranchByIntron

public java.lang.String getBranchByIntron(java.lang.String intronKey)

getBranchU12

public java.util.List<SpliceSiteBranchU12> getBranchU12(java.lang.String donorAcceptor)

Add a SpliceSiteBranchU12 for this donor-Acceptor pair

getDonor

public java.lang.String getDonor(int i)

getDonorAccPairSize

public int getDonorAccPairSize()

getDonorByIntron

public java.lang.String getDonorByIntron(java.lang.String intronKey)

getIntronKeySet

public java.util.Set<java.lang.String> getIntronKeySet()

setDebug

public void setDebug(boolean debug)

setGenomeFasta

public void setGenomeFasta(java.lang.String genomeFasta)

setTranscriptSet

public void setTranscriptSet(TranscriptSet transcriptSet)

setVerbose

public void setVerbose(boolean verbose)