Class SpliceTypes

java.lang.Object
org.snpeff.spliceSites.SpliceTypes

public class SpliceTypes extends Object
Analyze sequences from splice sites
Author:
pcingola
  • Field Details

    • 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:
    • THRESHOLD_COUNT

      public static final int THRESHOLD_COUNT
      See Also:
    • THRESHOLD_P

      public static final double THRESHOLD_P
      See Also:
  • Constructor Details

    • SpliceTypes

      public SpliceTypes(Config config)
  • Method Details

    • 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
    • analyzeAndCreate

      public boolean analyzeAndCreate()
      Analyze and create conserved splice sites donor-acceptor pairs.
    • bestU12Score

      public Tuple<Double,Integer> bestU12Score(String seq)
      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
    • 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(String outputDir)
      Create one fasta file for each donor-acceptor pair
    • getAcceptor

      public String getAcceptor(int i)
    • getAcceptorsByIntron

      public String getAcceptorsByIntron(String intronKey)
    • getBranchByIntron

      public String getBranchByIntron(String intronKey)
    • getBranchU12

      public List<SpliceSiteBranchU12> getBranchU12(String donorAcceptor)
      Add a SpliceSiteBranchU12 for this donor-Acceptor pair
    • getDonor

      public String getDonor(int i)
    • getDonorAccPairSize

      public int getDonorAccPairSize()
    • getDonorByIntron

      public String getDonorByIntron(String intronKey)
    • getIntronKeySet

      public Set<String> getIntronKeySet()
    • setDebug

      public void setDebug(boolean debug)
    • setGenomeFasta

      public void setGenomeFasta(String genomeFasta)
    • setTranscriptSet

      public void setTranscriptSet(TranscriptSet transcriptSet)
    • setVerbose

      public void setVerbose(boolean verbose)