Package fork.lib.bio.anno.genomic

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

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        this.od=od;
        init();
    }
   
protected void init() throws Exception {
    dis = new BedGraphBuffer(f).getDistributionNonZero();
    File odsub= new File(od+"/bgsub");
    odsub.getAbsoluteFile().mkdirs();
    outSub= new File(odsub+"/bgsub_"+ f.getName());
    outNorm= new File(od+"/norm_"+f.getName());
}
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    BufferedWriter bw= new BufferedWriter(new FileWriter(outSub));
    BedGraphExporter.writeTitle(bw, FileName.getBaseName(outSub));
   
    LandscapeBuffer lbb= new BedGraphBuffer(f);
    String[] chrs= lbb.getUnsortedChromosomeList();
    for( int k=0; k<chrs.length ; k++ ){
        String chr = chrs[k];
        System.out.print(chr+"  ");
        ArrayList<Region> rs= lbb.getLandscape2DForChromosome(chr).getRegions();
        for( int i=1; i<rs.size() ; i++ ){
            Region r= rs.get(i);
            double val= Double.parseDouble(r.attribute().toString());
            int v= (int) (val-thr);
            if(v>0 ){
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public static void toDiff(File f, File ref, File out) throws Exception{
    LandscapeBuffer lb= new BedGraphBuffer(f);
    LandscapeBuffer lbref= new BedGraphBuffer(ref);

    LandscapeComparatorBuffer lc = new LandscapeComparatorBuffer(lb, lbref) {
            @Override
            public double newValue(double v, double refv) {
                return new Double( (double)Math.round( (v- refv) * 1000)/1000  );
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    File f= new File("out/score/set/sacCer1-xu/scan/intra_300_0_10_51.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    String s= "884-rrp6d-wt";
    LandscapeBuffer lbf= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_for.wig"));
    LandscapeBuffer lbr= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_rev.wig"));
    System.out.println(1);
   
    LinkAntisense ll= new LinkAntisense(gb, lbf, lbr);
    //LinkAntisense ll= new LinkAntisense(gb, null, null);
    ll.writeToFile(new File("out/score/set/sacCer1-xu/scan/linkAnti_"+FileName.getBaseName(f) +".bed"));
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    NormChipSeqRPM.toRatio(f, in, outRat);
}

public void subtract()throws Exception {
   
    Distribution dis0 = new BedGraphBuffer(outRat).getDistributionNonZero();
    Distribution dis= dis0.subsetHigherThan(1);
    dis= dis.subsetLowerOrEqualTo(dis.quantileBoundaries(10).get(5));
   
   
    double mean= dis.mean();
    double sd= dis.standartDeviation();
    double rat= mean+ 1.2 *sd;
   
    System.out.println("m: "+ mean+"   sd: "+sd+"  rat: "+rat);
   
    //double rat= 2.5;
   
    /*
    while(true){
        try{
            String l= new BufferedReader(new InputStreamReader(System.in)).readLine();
            String[] ss= l.split(" ");
            int n= Integer.parseInt(ss[0]);
            int tar= Integer.parseInt(ss[1]);
            if(n==-1){
                break;
            }
            ArrayList<Double> qs= dis.quantileBoundaries(n);
            Distribution ndis= dis.subsetLowerOrEqualTo(qs.get(tar));
            System.out.println("mean: "+ ndis.mean()+"   sd: "+ ndis.standartDeviation());
           
        }catch(Exception e){}
    }
    */
   
   
   
    LandscapeBuffer lbf= new BedGraphBuffer(f);
    LandscapeBuffer lbi= new BedGraphBuffer(in);
    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);
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public void subtract2()throws Exception {
    Distribution dis= new BedGraphBuffer(outSub).getDistributionNonZero();
    dis= dis.subsetLowerThan(dis.quantileBoundaries(10).get(7));
    double med= dis.median();
    double sd= dis.standartDeviation();
    double thr= med+ sd* 2;
    System.out.println("med: "+ med+"   sd: "+ sd+"     "+ thr);

    BufferedWriter bw= new BufferedWriter(new FileWriter(outSub2));
    BedGraphExporter.writeTitle(bw, FileName.getBaseName(outSub2));
   
    LandscapeBuffer lbb= new BedGraphBuffer(f);
    String[] chrs= lbb.getUnsortedChromosomeList();
    for( int k=0; k<chrs.length ; k++ ){
        String chr = chrs[k];
        System.out.print(chr+"  ");
        ArrayList<Region> rs= lbb.getLandscape2DForChromosome(chr).getRegions();
        for( int i=1; i<rs.size() ; i++ ){
            Region r= rs.get(i);
            double val= Double.parseDouble(r.attribute().toString());
            if(val>thr){
                double v= val-thr;
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    NormChipSeqZero nn= new NormChipSeqZero();
    nn.init(lb);

   
    File of1= new File(od+"/subtract_"+tag+".wig");
    NormChipSeqRPM.subtract(new BedGraphBuffer(f),new BedGraphBuffer(inf), of1, "subtract_"+tag, nn.depthFactor);
    File of2 = new File(od+"/norm_"+tag+".wig");
    NormChipSeqRPM.normalise(new BedGraphReader(of1).getLandscapeBuilder(), of2, FileName.getBaseName(of2), nn.normFactor);
    System.out.println();
   
}
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    new BedGraphExporter(tr.toLandscapeBuilder(), tit).writeToFile(out);
}
   
   
public static void unlog(File wig, File out, String tit) throws Exception{
    LandscapeBuffer lb= new BedGraphBuffer(wig);
    BufferedWriter bw= new BufferedWriter(new FileWriter(out));
    BedGraphExporter.writeTitle(bw, tit);
    String[] chrs= lb.getUnsortedChromosomeList();
    for( int i=0; i<chrs.length ; i++ ){
        String chr= chrs[i];
        LandscapeBuilder lbt= new LandscapeBuilder();
        lbt.addAll(chr, lb.getLandscape2DForChromosome(chr));
        new LandscapeTransformer(lbt).unlog(Math.E);
        BedGraphExporter be= new BedGraphExporter(lbt);
        be.appendToFile(bw);
    }
    bw.close();
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    be.writeToFile(of);
}
   

public static void toRatio(File f, File ref, File out) throws Exception{
    LandscapeBuffer lb= new BedGraphBuffer(f);
    LandscapeBuffer lbref= new BedGraphBuffer(ref);

    LandscapeComparatorBuffer lc = new LandscapeComparatorBuffer(lb, lbref) {
            @Override
            public double newValue(double v, double refv) {
                return new Double( (double)Math.round(v/refv * 1000)/1000  );
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        NormChipSeqRPM nn= new NormChipSeqRPM(rnum);
        LandscapeBuilder lb = new BedGraphReader(rf).getLandscapeBuilder();
        nn.init(lb);
       
        File of1= new File(subtd+"/subtract_"+otag+".wig");
        nn.subtract(new BedGraphBuffer(f),new BedGraphBuffer(inf), of1, "subtract_"+tag, nn.depthFactor);
       
        File of2 = new File(od+"/norm_"+otag+".wig");
        nn.normalise(new BedGraphReader(of1).getLandscapeBuilder(), of2, FileName.getBaseName(of2), nn.seqDepth);
        System.out.println();
    }
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Related Classes of fork.lib.bio.anno.genomic.BedGraphBuffer

  • data.cerevisiae.inhouse.a_norm.NormChipChipSignal
  • data.cerevisiae.inhouse.a_norm.NormChipSeqRPM
  • data.cerevisiae.inhouse.a_norm.NormChipSeqZero
  • data.cerevisiae.lee2007.NormToLee
  • data.cerevisiae.region.scan.LinkAntisense
  • data.cerevisiae.region.scan.ScanIntra
  • data.cerevisiae.test.ratio.ToRatio
  • data.human.inhouse.norm.NormChipSeq
  • data.human.statham2014mods.NormTest
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