Package fork.lib.bio.anno.genomic.region

Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder

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    File fr= new File(d+"/score_-_refine-5000_novel_genes.fpkm_tracking.bed");
    File of= new File(d+"/novel.bed");
   
    BufferedReader brf= new BufferedReader(new FileReader(ff));
    BufferedReader brr= new BufferedReader(new FileReader(fr));
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    String lf;
    while((lf=brf.readLine())!=null){
        String lr=brr.readLine();
        String[] ssf= lf.split("\t");
        String[] ssr= lr.split("\t");
        double vf= Double.parseDouble(ssf[4]);
        double vr= Double.parseDouble(ssr[4]);
        String chr= ssf[0];
        int low= Integer.parseInt(ssf[1]);
        int high= Integer.parseInt(ssf[2]);
        String id= ssf[3];
        if(!(vf==0 && vr==0)){
            DirectionalGenomicRegion dr;
            if(vf>vr){
                dr= new DirectionalGenomicRegion(chr, '+', low, high);
                dr.setValue(vf);
            }else{
                dr= new DirectionalGenomicRegion(chr, '-', low, high);
                dr.setValue(vr);
            }
            dr.setID(id);
            gbout.add(dr);
        }
    }
    brf.close();
    brr.close();
   
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    File od= new File(dir+"/anno/bed/sacCer1-xu/cds");
   
    int len= 150;
    int side= 300;
   
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
    gb= gm.getGenicRegions(side, side);
   
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        DirectionalGenomicRegion gr= (DirectionalGenomicRegion)it.next();
        int i=0;
        double low= gr.low;
        while( (low+len)<gr.high ){
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public void writeToDir(File od)throws Exception {
    ArrayList<File> fs= GenerateGenic.getFiles();
    for( int i=0; i<fs.size(); i++ ){
        File f= fs.get(i);
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
        LandscapeScoring ls= new LandscapeScoring(lb, gb){
        protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
            return new double[]{Landscape2DBuffer.getArea(bufs, gr) / (gr.getRange()+1) *1000 };
        }

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    File rd= new File(dir+"/data/human_magnus/rna/norm");
    File rfor= new File(rd+"/norm_mcf7_rna3_time-"+time+"_hg19_for.wig");
    File rrev= new File(rd+"/norm_mcf7_rna3_time-"+time+"_hg19_rev.wig");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbnew= new GenomicRegionsModifier(gb).setStrand(strand);
   
    LandscapeBuilder lbf= new BedGraphReader(rfor).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(rrev).getLandscapeBuilder();
   
    LandscapeScoringStrand ls= new LandscapeScoringStrand(lbf, lbr, gbnew);
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    File cd= new File(dir+"\\data\\human_magnus\\h2az\\norm");
    File d= new File(dir+"/data\\human_magnus\\h2az\\norm\\peak/merge");
    File od= new File(d+"/scoreChipAbs");
    File rf= new File(d+"/merge.bed");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    File[] fs= cd.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("wig")){
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    File d= new File(dir+"/data/human_magnus/rna/cuff/time-5");
    File f= new File(d+"/novel_genes.fpkm_tracking.bed");
    File of= new File(d+"/refine-"+ side+"_"+ f.getName() );
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbref= new BedReader(new File(dir+"/anno/hg19_ensGene_exon.bed")).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbrefs= new GenomicRegionsModifier(gbref).getExtendedRegions(side, side);
   
   
    GenomicRegionsComparator gc= new GenomicRegionsComparator(gb, gbrefs);
    new BedExporter( gc.getNonIntersection() ).writeToFile(of);
   
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    File[] fs= d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("bed") && !f.getName().equals(out.getName()) ){
            System.out.println(f);
            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            mer.mergeNoSort(gb);
        }
        mer.sort();
        new BedExporter(mer.getMergedGenomicRegionsBuilder()).writeToFile(out);
    }
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    File[] fs= d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("bed") && !f.getName().equals(out.getName()) ){
            System.out.println(f);
            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            mer.mergeNoSort(gb);
        }
        mer.sort();
    }
   
    GenomicRegionsBuilder gbout= mer.getMergedGenomicRegionsBuilder();
    new BedExporter(gbout).writeToFile(out);
   
}
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protected void writeToFile(File out)throws Exception {
    GenomicRegionsComparator comp= new GenomicRegionsComparator(peaks, in);
    GenomicRegionsBuilder gbOverlapIn= comp.getIntersection();
    GenomicRegionsComparator comp2= new GenomicRegionsComparator(gbOverlapIn, ex);
    GenomicRegionsBuilder gbOverlapInNotEx = comp2.getNonIntersection();
   
    new BedExporter(gbOverlapInNotEx).writeToFile(out);
}
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    File od= new File(d+"/novelIntron");

    int side= -1000;

    SplicedBedReader sr= new SplicedBedReader(annof);
    GenomicRegionsBuilder gbin= sr.getAllIntrons();
    GenomicRegionsModifier gmin= new GenomicRegionsModifier(gbin);
    GenomicRegionsBuilder gbinside= gmin.getExtendedRegions(side, side);
    GenomicRegionsBuilder gbex= sr.getAllExons();
    GenomicRegionsModifier gmex= new GenomicRegionsModifier(gbex);
    GenomicRegionsBuilder gbexside= gmex.getExtendedRegions(500, 500);
   
   
    File[] fs= d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File pf= fs[i];
        if(FileName.getExt(pf).equals("bed")){
            GenomicRegionsBuilder gbpeak= new BedReader(pf).getGenomicRegionsBuilder();
            GetNovelPeaksIntron gn= new GetNovelPeaksIntron(gbpeak, gbinside, gbexside);

            File out= new File(od+"/novel_"+ pf.getName());
            gn.writeToFile(out);
        }
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Related Classes of fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder

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  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
  • data.cerevisiae.inhouse.a_norm.NormRNASeq
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.a_score.ScoreRNAAnti
  • data.cerevisiae.inhouse.a_score.ScoreRNAGene
  • data.cerevisiae.inhouse.a_score.ScoreRNAGeneRead
  • data.cerevisiae.inhouse.chip.ChipChipRemoveExtreme
  • data.cerevisiae.inhouse.spikein.ScoreSpike
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