Package fork.lib.bio.anno.genomic

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

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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{
                double max= 0;
                for(int i=0; i<bufs.size() ; i++){
                    double v= (Double) bufs.get(i).attribute();
                    if(v>max){
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    int[]ss= new int[]{150, 300, 450};
    for( int i=0; i<ss.length ; i++ ){
        int s= ss[i];
        File od= new File(dir+"/anno/bed/"+org+"/set/set_"+s);

        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
        GenerateOverviewSet gg= new GenerateOverviewSet(gb, s);
        gg.writeToDirectory(od, org);

    }
}
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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("bed")){
            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
            gb= gm.getThreePrimeEnds(150, 0); /////////// modify this
            FastaSequenceExtractor fe= new FastaSequenceExtractor(fastaf, gb, null);

            File of= new File(od+"/"+tag+"_"+FileName.getBaseName(f)+".fasta");
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    File rnad= new File(dir+"/data/human_magnus/rna/norm");
    File od= new File(d+"/scoreRNA");
    File f= new File(d+"/merge.bed");
   
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    File[] rfs= rnad.listFiles();
    HashSet<String> tags= new HashSet<>();
    for( int i=0; i<rfs.length; i++ ){
        File rf= rfs[i];
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    File d= new File(dir+"/anno");
    File f= new File(d+"/xu_2009_orfs_uncorrected.bed");
   
    File out= new File(d+"/xu_2009_orfs.bed");
    CorrectXu2009 cc= new CorrectXu2009(new BedReader(f).getGenomicRegionsBuilder());
    cc.writeToFile(out);
   
}
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        init();
    }
   
   
protected void init() throws Exception{
    gb= new BedReader(file).getGenomicRegionsBuilder();
   
    CrossAnno cr= new CrossAnno(link,0,1);
    Iterator<GenomicRegion> it = gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
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    File od= new File(dir+"/anno/bed/"+org+"/200");
   
    BedReaderParam par= new BedReaderParam();
    par.ifDirectional=true;
   
    GenomicRegionsBuilder gb= new BedReader(f, par).getGenomicRegionsBuilder();
   
    Generate gg= new Generate(gb);
    gg.writeToDirectory(od, org);
}
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    File d = new File(dir+"/other_datasets/lee_2007_nucleosome");
    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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        //new File(dir+"/other_datasets/ranjan2013_swr1-chip/swr1-chip_wt.wig"),
        //new File(dir+"/other_datasets/ranjan2013_swr1-chip/swr1-chip_htz1d.wig"),
    };
   
    File an= new File(dir+"/anno/xu_2009_orfs.bed");
    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();
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    int[] offs= new int[]{0, 50, 100};
   
    for( int i=0; i<offs.length; i++ ){
        int off= offs[i];
        GenerateLen gg= new GenerateLen(
                new BedReader(new File(dir+"/anno/sacCer1_chr.bed")).getGenomicRegionsBuilder(),
                len, off );
        gg.writeToFile(new File(dir+"/anno/bed/len/len_"+len+"_off_"+off+".bed"));
    }
   
   
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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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