Package org.snpeff.spliceSites
Class SpliceTypes
java.lang.Object
org.snpeff.spliceSites.SpliceTypes
Analyze sequences from splice sites
- Author:
- pcingola
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic int
static int
static final int
static final double
static final double
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionaddBestU12Score
(Transcript tr, String chrSeq, String donorAcceptor, int intronStart, int intronEnd) Calculate the best U12 score.boolean
Analyze and create conserved splice sites donor-acceptor pairs.bestU12Score
(String seq) Find the best score for PWM matrix in U12 branch pointsdouble
branchU12Threshold
(double thresholdU12Percentile) Calculate threshold of U12 PWM scores Pick the score that gives a 'thresholdU12Percentile'.void
createSpliceFasta
(String outputDir) Create one fasta file for each donor-acceptor pairgetAcceptor
(int i) getAcceptorsByIntron
(String intronKey) getBranchByIntron
(String intronKey) getBranchU12
(String donorAcceptor) Add a SpliceSiteBranchU12 for this donor-Acceptor pairgetDonor
(int i) int
getDonorByIntron
(String intronKey) void
setDebug
(boolean debug) void
setGenomeFasta
(String genomeFasta) void
setTranscriptSet
(TranscriptSet transcriptSet) void
setVerbose
(boolean verbose)
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Field Details
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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:
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THRESHOLD_COUNT
public static final int THRESHOLD_COUNT- See Also:
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THRESHOLD_P
public static final double THRESHOLD_P- See Also:
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Constructor Details
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SpliceTypes
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Method Details
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addBestU12Score
public Tuple<Double,Integer> addBestU12Score(Transcript tr, String chrSeq, 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<Double, Integer> having the best score and best position
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analyzeAndCreate
public boolean analyzeAndCreate()Analyze and create conserved splice sites donor-acceptor pairs. -
bestU12Score
Find the best score for PWM matrix in U12 branch points- Parameters:
seq
-- Returns:
- A Tuple<Double, Integer> having the best score and best position
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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
Create one fasta file for each donor-acceptor pair -
getAcceptor
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getAcceptorsByIntron
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getBranchByIntron
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getBranchU12
Add a SpliceSiteBranchU12 for this donor-Acceptor pair -
getDonor
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getDonorAccPairSize
public int getDonorAccPairSize() -
getDonorByIntron
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getIntronKeySet
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setDebug
public void setDebug(boolean debug) -
setGenomeFasta
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setTranscriptSet
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setVerbose
public void setVerbose(boolean verbose)
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