Package fork.lib.bio.anno.genomic

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

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        File f= new File(d+"/peak_norm_wig_mcf7_chip-h2az_"+ttag+".bed");
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
       
        //System.out.println("xxx"); System.exit(1);
       
        LandscapeBuilder lbf= new BedGraphReader(new File(rnad+"/norm_"+tag+"_for.wig")).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(new File(rnad+"/norm_"+tag+"_rev.wig")).getLandscapeBuilder();
       
        File od= new File(d+"/scoreRNAEach");
        File outf= new File(od+"/score_"+tag+"_for.bed");
        File outr= new File(od+"/score_"+tag+"_rev.bed");
       
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    File anno= new File(dir+"/anno/xu_2009_orfs.bed");
    File forf= new File(rd+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_for.wig");
    File revf= new File(rd+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_rev.wig");
   
   
    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
    GenomicRegionsBuilder gb= new GenomicRegionsModifier(new BedReader(anno).getGenomicRegionsBuilder()).getThreePrimeEnds(150, 0);
   
   
    AssoTranscriptionThree ass= new AssoTranscriptionThree(gb, lbf, lbr);
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    File rf= new File(dir+"/anno/bed/sacCer1-xu/cds/xu_2009_orfs_cds_300_150.bed");
    File datd= new File(dir+"/data/chip-seq/norm");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    LandscapeBuilder lb= new BedGraphReader(new File(datd+"/norm_wig_chip_htz1-anti660_772-wt_sd_20131104-r1_pe1_sacCer1.wig")).getLandscapeBuilder();
   
   
    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) / 100 };
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    File rd= new File(dir+"/data/chip-seq/norm/peak_new/rand/cds");
   
    GenomicRegionsBuilder gb= new BedReader(new File(dir+"/anno/bed/sacCer1-xu/cds/xu_2009_orfs_cds_300_150.bed")).getGenomicRegionsBuilder();
   
    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
   
    new RandomNew(3044, rd, lbf, lbr, gb);
}
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    while(it.hasNext()){
        String tag= it.next();
        System.out.println(tag);
        File ff= new File(d+"/"+tag+"_for.wig");
        File fr= new File(d+"/"+tag+"_rev.wig");
        LandscapeBuilder lbf= new BedGraphReader(ff).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(fr).getLandscapeBuilder();
        ScoreRNAGene ss= new ScoreRNAGene(lbf, lbr, tag);
        File odt= new File(od+"/"+tag);
        ss.writeToDir(odt);
    }
   
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    File zf= new File(dir+"/anno/bed/sacCer1-xu/cds/xu_2009_orfs_cds_300_150.bed");
    File forf= new File(rd+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_for.wig");
    File revf= new File(rd+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_rev.wig");
   
   
    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
    GenomicRegionsBuilder gb= new BedReader(zf).getGenomicRegionsBuilder();
   
   
    AssoTranscriptionThree ass= new AssoTranscriptionThree(gb, lbf, lbr);
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    File rd= new File(dir+"/data/chip-seq/norm/peak_new/rand/three");
   
    GenomicRegionsBuilder gb= new GenomicRegionsModifier(new BedReader(anno).getGenomicRegionsBuilder()).getThreePrimeEnds(150, 0);
   
    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
    new RandomNew(927, rd, lbf, lbr, gb);
}   
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    for( int i=0; i<fs.length; i++ ){
    //for( int i=0; i<2; i++ ){
        File f= fs[i];
        System.out.println(f);
        if(FileName.getExt(f).equals("wig")){
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            String tag= FileName.getBaseName(f);
            ScoreChipSeqGene ss= new ScoreChipSeqGene(lb, tag);
            File odt= new File(od+"/"+tag);
            ss.writeToDir(odt);
        }
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    BufferedWriter bw= new BufferedWriter(new FileWriter(outSub));
    BedGraphExporter.writeTitle(bw, FileName.getBaseName(outSub));
   
    String[] chrs= lbf.getUnsortedChromosomeList();
    for( int i=0; i<chrs.length; i++ ){
        LandscapeBuilder lbout= new LandscapeBuilder();
        String chr= chrs[i];
        System.out.print(chr+"  ");
        ArrayList<Region> frs= lbf.getLandscape2DForChromosome(chr).getRegions();
        ArrayList<Region> irs= lbi.getLandscape2DForChromosome(chr).getRegions();
        RegionBuffer buf= new RegionBuffer(irs);
        for( int j=0; j<frs.size(); j++ ){
            Region fr= frs.get(j);
            ArrayList<Region> bufrs= buf.reloadAndGetList(fr);
            double ival= RegionBuffer.getOverlap(bufrs, fr) / (fr.getRange()+1);
            double fval= (double)fr.attribute();
            double nv= fval - ival*rat;
           
            //System.out.println(fval+"    "+ ival+"   "+ fr.getRange());
            nv= nv<0 ? 0 : nv;
            fr.setAttribute(nv);
            lbout.add(chr, fr);
        }
        BedGraphExporter be= new BedGraphExporter(lbout);
        be.appendToFile(bw);
    }
    bw.close();
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}



public void removeShort()throws Exception {
    LandscapeBuilder lb= new BedGraphReader(outSub2).getLandscapeBuilder();
    LandscapeTransformer lt= new LandscapeTransformer(lb);
    lt.selectLength(150, Integer.MAX_VALUE);
    double sum= lb.totalArea();
    double fac= sum/Math.pow(10, 8);
    lt.divideBy( fac );
    new BedGraphExporter(lb).writeToFile(out);
}
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Related Classes of fork.lib.bio.anno.genomic.LandscapeBuilder

  • data.cerevisiae.at.Score
  • data.cerevisiae.auerbach2013_polii.Score
  • data.cerevisiae.ConsToWig
  • data.cerevisiae.histmod.cai2011.Score
  • data.cerevisiae.histmod.cai2011.ToWig
  • data.cerevisiae.histmod.guillemett2011_h3k4.Unlog
  • data.cerevisiae.histmod.guillemette2011.Score
  • data.cerevisiae.histmod.guillemette2011.ToWig
  • data.cerevisiae.histmod.kirmizis2009.Score
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
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