Package fork.lib.bio.anno.genomic

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

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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);
       
        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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    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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        String samp= samps[i];
       
        File ff= new File(datd+"/strand_rna_"+samp+"_sacCer1_for.wig");
        File rf= new File(datd+"/strand_rna_"+samp+"_sacCer1_rev.wig");
       
        LandscapeBuilder lbf= new BedGraphReader(ff).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(rf).getLandscapeBuilder();
       
        NormRNASeq nn= new NormRNASeq(lbf, lbr, gb);
        nn.writeToFiles(
                new File(od+"/norm_"+ff.getName()),
                new File(od+"/norm_"+rf.getName())
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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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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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