Package fork.lib.bio.anno.genomic

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

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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);
        }
    }
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    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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    String org= "sacCer1-xu";
    File f= new File(d+"/unlog_analyzed_data_complete_bw20.bar");
   
   
    LandscapeBuilder lb= new BarReader(f).getLandscapeBuilder();
    ScoreChipGene sc= new ScoreChipGene(lb, org, od, "lee2007");
   
   
   
   
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    for( int k=0; k<samps.length ; k++ ){
        String samp= samps[k];
        File datf= new File(wd+"/norm_"+samp+".wig");
        LandscapeBuilder lb= new BedGraphReader(datf).getLandscapeBuilder();
       
        File ood= new File(od+"/"+samp);
        ScoreChipGene sc= new ScoreChipGene(lb, org, ood, samp);
       
        System.out.println(samp);
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        File rf= new File(ratiod+"/ratio_"+otag+".wig");
        toRatio(f, inf, rf);
       
       
        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);
       
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    for( int k=0; k<samps.length ; k++ ){
        String samp= samps[k];
        File f= new File(datd+"/norm_wig_chip_"+samp+"_sacCer1.wig");

        LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
       
        int rlen= StatRetriever.getReadLen("chip_"+samp);
        System.out.println(samp+"    rlen:"+ rlen);

        File od= new File(outd+"/"+samp);
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    String org= "sacCer1-xu";
    File f= new File(d+"/ratio-lee2007_norm_wig_chip_742-wt_r2_sacCer1.wig");
   
   
    LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
   
    ScoreChipGene sc= new ScoreChipGene(lb, org, od, "742-lee2007");
   
   
}
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    File dir= Dirs.getFile("dir");
    File f= new File(dir+"/data/chip-seq/norm/norm_wig_chip_htz1-anti660_772-wt_sd_20131104-r1_pe1_sacCer1.wig");
    File od= new File(dir+"/data/chip-seq/norm/peak3");
   
   
    LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
    PeakIdentifier pi= new PeakIdentifier(lb, null);
   
    pi.getPeaks().writeToFileBed(new File(od+"/peak_"+FileName.getBaseName(f)+".bed"));
   
   
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    Iterator<String> it= tags.iterator();
    while(it.hasNext()){
        String samp= it.next();
        System.out.println(samp);
        LandscapeBuilder lbf= new BedGraphReader(new File(datd+"/strand_rna_"+samp+"_sacCer1_for.wig")).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(new File(datd+"/strand_rna_"+samp+"_sacCer1_rev.wig")).getLandscapeBuilder();
       
       
        int rlen= StatRetriever.getReadLen("rna_"+samp)-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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