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
All Methods Instance Methods Concrete Methods 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 pointsdouble
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 pairjava.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 pairjava.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)
-
-
-
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)
-
-