Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.LandscapeScoring

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    od.mkdirs();
    File[] fs= ScoreChipGene.files(org);
    for(int i=0; i<fs.length ; i++){
        File f=fs[i];
        System.out.println(f);
        ls= new LandscapeScoring(lb, new BedReader(f).getGenomicRegionsBuilder()){
            protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                return new double[]{Landscape2DBuffer.getArea(bufs, gr) / ((gr.getRange()+1)/1000) / rlen };
            }
        };
        File out= new File(od+"/"+samp+"_"+FileName.getBaseName(f)+".bed");
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    }
   
   
protected void start() throws Exception{
    LandscapeScoring ls= new LandscapeScoring(lb, gb){
        protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
            return Landscape2DBuffer.getLandscape(bufs, gr);
        }
    };
    ArrayList<LandscapeScoringResultEntry> ress= ls.getResultEntries();
    for( int i=0; i<ress.size() ; i++ ){
        LandscapeScoringResultEntry res= ress.get(i);
        DirectionalGenomicRegion gr= (DirectionalGenomicRegion)res.gr;
        double[] vs= res.scores;
        int slow= gr.isOnForwardStrand() ? side5: side3,
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public void writeToFile(File out) throws Exception{
    LandscapeScoring ls= new LandscapeScoring(lb, gbout);
    LandscapeScoringResultEntry.writeToBedFile(ls.getResultEntries(), out);
}
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Related Classes of fork.lib.bio.anno.genomic.LandscapeScoring

  • data.cerevisiae.inhouse.a_score.ScoreChipGene
  • data.cerevisiae.inhouse.a_score.ScoreChipSeqGene
  • data.cerevisiae.inhouse.a_score.ScoreLen
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.spikein.ScoreSpike
  • data.cerevisiae.lee2007.pref.ScoreWindow
  • data.cerevisiae.region.scan.AntisenseFraction
  • data.cerevisiae.region.scan.ScanIntra
  • data.cerevisiae.region.wt4krlen.ScoreLen
  • data.cerevisiae.region.zpeak.trsc_asso_new.cds.Score
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