Package fork.lib.bio.anno.genomic

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

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    od.mkdirs();
    File[] fs= files(org);
    for(int i=0; i<fs.length ; i++){
        File f=fs[i];
        System.out.println(f);
        ls= new LandscapeScoring(lb, new BedReader(f).getGenomicRegionsBuilder()){
            protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                return new double[]{Landscape2DBuffer.getArea(bufs, gr) /100 / ((gr.getRange()+1)/1000) };
            }
        };
        File out= new File(od+"/"+samp+"_"+FileName.getBaseName(f)+".bed");
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    File d= new File(dir+"/anno/bed/sacCer1");
    File anno = new File(dir+"/anno/sacCer1_chr.bed");
   
    int len= 10;
   
    GenomicRegionsBuilder gb= new BedReader(anno).getGenomicRegionsBuilder();
   
    GenerateWindowsNonOverlapping gg= new GenerateWindowsNonOverlapping(gb, len);
    gg.writeToFile(new File(d+"/window/non-ol_"+ len+"_"+FileName.getBaseName(anno)+".bed"));
   
}
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    od.mkdirs();
    File[] fs= ScoreChipGene.files(org);
    for(int i=0; i<fs.length ; i++){
        File f=fs[i];
        System.out.println(f);
        ls= new LandscapeScoring(lb, new BedReader(f).getGenomicRegionsBuilder()){
            protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                return new double[]{Landscape2DBuffer.getArea(bufs, gr) / ((gr.getRange()+1)/1000) / rlen };
            }
        };
        File out= new File(od+"/"+samp+"_"+FileName.getBaseName(f)+".bed");
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public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
    File d = new File(dir+"/other_datasets/lee_2007_nucleosome/pref");
    File f= new File(d+"/score_non-ol_10_sacCer1_chr.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    int binn = 10;
   
    Bin  bb= new Bin(gb, binn);
    bb.writeToDir(d);
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            tags.add(t);
        }
    }
   
    File outd= new File(datd+"/score/"+ty);
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();
   
       
    Iterator<String> it= tags.iterator();
    while(it.hasNext()){
        String samp= it.next();
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        "1054-wt-gdna_sd-ura_20140313-r2_pe1"
    };
   
    File od= new File(datd+"/norm");
   
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();
   
       
    for( int i=0; i<samps.length ; i++ ){
        String samp= samps[i];
       
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    File datf= new File(dir+"/data/chip-seq/norm/norm_"+samp+".wig");
   

    LandscapeBuffer lb= new BedGraphBuffer(datf);
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();

   
   
    ScanIntra si = new ScanIntra(gb, lb);
    si.side5= s5;
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    File dir= new File("/home/forksapien/mystudy/phd/files");
    //File dir= new File("G:/mystudy/phd/files");
   
    File f= new File(dir+"/anno/sgdGene_sacCer1.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    File out = new File(dir+"/anno/clas/clas_chr.txt");
    out.getParentFile().mkdirs();
    BufferedWriter bw= new BufferedWriter(new FileWriter(out));
    String[] chrs= gb.getChromosomeList();
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public void writeToFile(File of)throws Exception{
    LandscapeScoringStrand ls= new LandscapeScoringStrand(
            new BarReader(ff).getLandscapeBuilder(),
            new BarReader(fr).getLandscapeBuilder(),
            new BedReader(anno).getGenomicRegionsBuilder()
            );
    ls.writeToBedFile(of);
}
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public void writeToFile(File of)throws Exception{
    LandscapeScoringStrand ls= new LandscapeScoringStrand(
            new BarReader(fr).getLandscapeBuilder(),
            new BarReader(ff).getLandscapeBuilder(),
            new BedReader(anno).getGenomicRegionsBuilder()
            );
    ls.writeToBedFile(of);
}
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Related Classes of fork.lib.bio.anno.genomic.BedReader

  • data.cerevisiae.at.ATContentBp
  • data.cerevisiae.histmod.kirmizis2009.ProbeMapper$ProbeMapperStrand
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
  • data.cerevisiae.inhouse.a_norm.NormRNASeq
  • data.cerevisiae.inhouse.a_score.ScoreChipGene
  • data.cerevisiae.inhouse.a_score.ScoreChipSeqGene
  • data.cerevisiae.inhouse.a_score.ScoreLen
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.a_score.ScoreRNAAnti
  • data.cerevisiae.inhouse.a_score.ScoreRNAGene
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