Package fork.lib.bio.anno.genomic

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

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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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    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");
    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();
   
}
View Full Code Here
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    for(int i=0; i<fs.length ; i++){
        String ty= fs[i];
        File f= new File(d+"/norm_"+ty+".wig");
        ChipChipRemoveExtreme cc= new ChipChipRemoveExtreme(
                new BedGraphReader(f).getLandscapeBuilder(), gb
                );
        File out= new File(od+"/ucsc_"+f.getName());
        cc.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")){
            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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    for( int i=0; i<samps.length ; i++ ){
    //forr( 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();
       
        for( int j=0; j<regfs.length ; j++ ){
            File f= new File(regd+"/"+ty+regfs[j]);
            String tag= FileName.getBaseName(f);
            File od= new File(outd+"/"+samp+"_antisense");
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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();
            ScoreFive ss= new ScoreFive(lb);
            File out= new File(od+"/score_"+ FileName.getBaseName(f)+".bed");
            ss.writeToFile(out);
        }
    }
View Full Code Here
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            String tag= samp+"_"+rep;
            File datf= new File(datd+"/norm_wig_chip_"+samp+"_"+rep+"_sacCer1.wig");
            //File datf= new File(datd+"/norm_"+samp+".wig");

            LandscapeScoring ls= new LandscapeScoring(
                new BedGraphReader(datf).getLandscapeBuilder(),
                new BedReader(reg).getGenomicRegionsBuilder()
                );

            File out = new File(outd+"/"+tag+"/set/score-len_"+ FileName.getBaseName(datf)+"_"+FileName.getBaseName(reg)+".bed");
            System.out.println(out);
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Related Classes of fork.lib.bio.anno.genomic.BedGraphReader

  • data.cerevisiae.auerbach2013_polii.Score
  • data.cerevisiae.histmod.cai2011.Score
  • data.cerevisiae.histmod.guillemett2011_h3k4.Unlog
  • data.cerevisiae.histmod.guillemette2011.Score
  • data.cerevisiae.histmod.kirmizis2009.Score
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
  • data.cerevisiae.histmod.liu2005_histmods.Score
  • data.cerevisiae.histmod.xue2012.Unlog
  • data.cerevisiae.inhouse.a_norm.NormChipChip
  • data.cerevisiae.inhouse.a_norm.NormChipSeqRPM
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