Package fork.lib.bio.anno.genomic

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

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    String tag= "h3k4ac";
   
    File f= new File(d+"/"+tag+"_guillemette2011.wig"), od= new File(d+"/score/"+tag);
   
   
    LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
    ScoreChipGene sc= new ScoreChipGene(lb, org, od, tag+"_guillemette2011");
   
   
}
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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 i=0; i<fs.size() ; i++ ){
        File f= fs.get(i);
        System.out.println(f);
        String chr= FileName.getBaseName(f);
        String[][] arr= new ReadTable(f).getTableAsArray();
        LandscapeBuilder lb= new LandscapeBuilder();
        int pp=0; double pv=0;
        for( int j=0; j<arr.length ; j++ ){
            String[] r= arr[j];
            int p= Integer.parseInt(r[0]);
            double v= Double.parseDouble(r[1]);
            if(pp!=0){
                Region reg= new Region(pp, p-1);
                reg.attr= (double)Math.round(pv*res)/res;
                lb.add(chr, reg);
            }
            pp=p; pv=v;
        }
       
        BedGraphExporter be= new BedGraphExporter(lb);
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    String org ="sacCer1-xu";
   
    //File f= new File(d+"/swr1-chip_wt.wig");
    File f= new File(d+"/swr1-chip_htz1d.wig");
   
    LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
    int rlen= 100;


    File od= new File(d+"/score/"+FileName.getBaseName(f));
    ScoreChipSeqGene sc= new ScoreChipSeqGene(lb, org, rlen, od, FileName.getBaseName(f));
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    File f= new File(d+"/analyzed_data_complete_bw20.wig");
    File od = new File(d+"/pref");
    File winf= new File(dir+"/anno/bed/sacCer1/window/non-ol_10_sacCer1_chr.bed");
   
    GenomicRegionsBuilder gb= new BedReader(winf).getGenomicRegionsBuilder();
    LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
   
    new LandscapeScoring(lb, gb).writeToBedFile(new File(od+"/score_"+winf.getName()));
   
}
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    GenomicRegionsBuilder gb= new BedReader(an).getGenomicRegionsBuilder();   
    gb= new GenomicRegionsModifier(gb).getFivePrimeEnds(300, 300);
   
    for(int i=0; i<fs.length ; i++){
        File f= fs[i];
        LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();

       
        File out= new File("out/line5_"+FileName.getBaseName(f)+".txt");

       
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    //for( int i=0; i<1 ; i++ ){
    for( int i=0; i<fs.length ; i++ ){
        String fn= fs[i];
        File f= new File(wd+"/"+fn+".wig");

        LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
        normalise(lb, new File(od+"/norm_"+f.getName()), "norm_"+fn);
    }
}
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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+"/strand_rna_"+samp+"_ercc-rna_for.wig")).getLandscapeBuilder();
       
        int rlen= StatRetriever.getReadLen("rna_"+samp)-1;
      
       
       
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        String t= ts[i];
        File rf= new File(d+"/peak_norm_wig_mcf7_chip-h2az_time-"+t+"_hg19.bed");
        GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
       
        File f= new File(cd+"/norm_wig_mcf7_chip-h2az_time-"+t+"_hg19.wig");
        LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
        File out= new File(od+"/chip_"+FileName.getBaseName(f)+".bed");
        ScoreChipNormEach ss= new ScoreChipNormEach(gb, lb);
        ss.writeToFile(out);

    }
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public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
    File rnad= new File(dir+"/data/rna-seq");
    File forf= new File(rnad+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_for.wig");
    File revf= new File(rnad+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_rev.wig");
    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
    File f= new File("E:\\muxingu\\mystudy\\phd\\files\\data\\chip-seq\\norm\\peak_new/3anti_asso-trsc_xu_2009_orfs.bed");
    //File f= new File("E:\\muxingu\\mystudy\\phd\\files\\data\\chip-seq\\norm\\peak_new\\rand\\three\\runs\\0/anit.bed");
   
    new Fuck2(f, lbf, lbr);
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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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