Class SpliceTypes


  • public class SpliceTypes
    extends java.lang.Object
    Analyze sequences from splice sites
    Author:
    pcingola
    • Field Detail

      • MAX_SPLICE_SIZE

        public static int MAX_SPLICE_SIZE
      • SIZE_BRANCH

        public static int SIZE_BRANCH
    • 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)