Package fork.lib.bio.anno.genomic

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

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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();
    }
   
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    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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    File rd= new File(dir+"/data\\human_magnus\\rna\\cuff/time-"+time);
   
    File zf= new File(zd+"/novel_mcf7_chip-h2az_time-"+time+"_peaks.bed");
    File rf= new File(rd+"/novel.bed");
   
    GenomicRegionsBuilder gbz= new BedReader(zf).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbr= new BedReader(rf).getGenomicRegionsBuilder();
   
   
   
    CountAssociated cc= new CountAssociated(gbz, gbr);
    cc.writeToDir(rd, FileName.getBaseName(zf));
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        this.probe=probe;
        this.std=std;
        init();
    }
protected void init() throws Exception{
    GenomicRegionsBuilder gba= new BedReader(anno).getGenomicRegionsBuilder();
    String[][] arr= new ReadTable(probe).getTableAsArray();
    double pp=-1; String pc="", pid=""; int ind=0;
    for(int i=0; i<arr.length ; i++){
        String[] r= arr[i];
        if(r[2].equalsIgnoreCase(std)){
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    double sum= 0;
    for( int i=0; i<fs.length ; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("bed")){
            gfs.add(f);
            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 };
                }
            };
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    File cd= new File(dir+"/data/human_magnus/rna/norm");
    File d= new File(dir+"/data\\human_magnus\\h2az\\norm\\peak/merge");
    File od= new File(d+"/scoreRNA");
    File rf= new File(d+"/merge.bed");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    File[] fs= cd.listFiles();
    HashSet<String> tags= new HashSet<>();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
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    //File f= new File(dir+"/anno/sgdGene_sacCer1.bed"); String org= "sacCer1";
    File f= new File(dir+"/anno/xu_2009_orfs.bed"); String org= "sacCer1-xu";
   
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    Iterator<GenomicRegion> it = gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        Integer len= (int) gr.getRange()+1;
        gr.setValue(len);
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Related Classes of fork.lib.bio.anno.genomic.BedReader

  • data.cerevisiae.at.ATContentBp
  • data.cerevisiae.histmod.kirmizis2009.ProbeMapper$ProbeMapperStrand
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
  • data.cerevisiae.inhouse.a_norm.NormRNASeq
  • 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.a_score.ScoreRNAAnti
  • data.cerevisiae.inhouse.a_score.ScoreRNAGene
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