Package fork.lib.bio.anno.genomic

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

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    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);
    ls.writeToBedFile(of);
   
   
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    File[] fs= cd.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("wig")){
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            File out= new File(od+"/chip_"+FileName.getBaseName(f)+".bed");
            ScoreMergeChipAbs ss= new ScoreMergeChipAbs(gb, lb);
            ss.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("wig") && f.getName().contains("for")){
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            File odt= new File(od+"/"+FileName.getBaseName(f));
            ScoreChipGene sc= new ScoreChipGene(lb, org, odt, FileName.getBaseName(f));
        }
    }
   
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    File lbf= new File(lbdir+"/norm-rpkm_wig_chip_772-wt_r1_2013Nov_001_sacCer1.wig");
    //File lbf= new File(lbdir+"/norm_wig_chip_742-wt_r1_sacCer1.wig");
    //File lbf= new File(lbdir+"/norm_wig_chip_743-4kr_r1_sacCer1.wig");
    //File lbf= new File(lbdir+"/norm_wig_chip_744-4kq_r1_sacCer1.wig");
   
    LandscapeBuilder lb= new BedGraphReader(lbf).getLandscapeBuilder();
   
    for( int i=0; i<ss.length ; i++ ){
        int s= ss[i];
        File out = new File("out/score/set/"+org+"/"+
        FileName.getBaseName(lbf) +"_"+org+"_"+s+".txt");
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    Iterator<String> it= tags.iterator();
    while(it.hasNext()){
        String tag=it.next();
        System.out.println(tag);
        LandscapeBuilder lbf= new BedGraphReader(new File(cd+"/"+tag+"_for.wig")).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(new File(cd+"/"+tag+"_rev.wig")).getLandscapeBuilder();
        ScoreRNAWithChipPeaks ss= new ScoreRNAWithChipPeaks(gb, lbf, lbr);
        File outf= new File(od+"/rna-for_"+tag+".bed");
        ss.writeToFile(outf);
       
        ss= new ScoreRNAWithChipPeaks(gb, lbr, lbf);
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    MarkReader mr= new MarkReader(f, "variableStep");
    MarkEntry en;
    LandscapeBuilder lb= new LandscapeBuilder();
    while((en=mr.nextEntry())!=null){
        String chr= en.tit.split("chrom=")[1];
       
        if(!chr.equals("chrM")){
            ArrayList<String> rs= en.chunk;
            int ps= 1;
            for( int i=0; i<rs.size(); i++ ){
                String l=rs.get(i);
                if(l.length()>0 && l.charAt(0)!='#'){
                    String[] ss= l.split("\t");
                    if(ss.length==2){
                        int p= Integer.parseInt(ss[0]);
                        double v= Double.parseDouble(ss[1]);
                        if(p<ps){
                            System.out.println(chr+"  "+ p+"  "+ v);
                        }
                        Region reg= new Region(ps, p);
                        reg.setAttribute(v);
                        lb.add(chr, reg);
                        ps= p+1;
                    }
                }
            }
        }
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    for( int i=0; i<samps.length ; i++ ){
    //for( int i=0; i<1 ; i++ ){
        String samp= samps[i];
       
        LandscapeBuilder lbf= new BedGraphReader(new File(datd+"/norm_strand_rna_"+samp+"_sacCer1_for.wig")).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(new File(datd+"/norm_strand_rna_"+samp+"_sacCer1_rev.wig")).getLandscapeBuilder();
        ScoreRNAGene sc= new ScoreRNAGene(gb, lbf, lbr);
        sc.writeToFile( new File(outd+"/"+samp+"_sense.bed") );
       
        sc= new ScoreRNAGene(gb, lbr, lbf);
        sc.writeToFile( new File(outd+"/"+samp+"_antisense.bed") );
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    File f= new File(wd+"/"+tag+".wig");
    File rf= new File(wd+"/ratio_"+tag+".wig");
   
   
    NormChipSeqRPM.toRatio(f, inf, rf);
    LandscapeBuilder lb = new BedGraphReader(rf).getLandscapeBuilder();
    NormChipSeqZero nn= new NormChipSeqZero();
    nn.init(lb);

   
    File of1= new File(od+"/subtract_"+tag+".wig");
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public void writeToFile(File out)throws Exception{
    LandscapeBuilder lbout= new LandscapeBuilder();
   
    String[] chrs= gbchr.getChromosomeList();
    for(int i=0; i<chrs.length ; i++){
        String chr= chrs[i];
        if(lb.containsChromosome(chr)){
            ArrayList<Region> rs= lb.getLandscape2DForChromosome(chr).getRegions();
            double lim= gbchr.getRegionsForChromosome(chr).get(0).high;
            for(int j=0; j<rs.size() ; j++){
                Region r= rs.get(j);
                if( r.lowerThan(lim) ){
                    lbout.add(chr,r);
                }
            }
        }
    }
   
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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("wig")){
            System.out.println(f);
            LandscapeBuilder lb= new BedGraphReader(f).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)
                    };
                }
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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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