Package fork.lib.bio.anno.genomic.region

Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder

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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();
    for( int i=0; i<chrs.length ; i++ ){
        String chr= chrs[i];
        bw.write(">"+chr+"\n");
        ArrayList<Region> al = gb.getRegionsForChromosome(chr);
        for( int j=0; j<al.size() ; j++ ){
            String n= ((GenomicRegion)al.get(j)).attr.toString();
            bw.write(n+"\n");
        }
    }
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            DirectionalGenomicRegion reg= new DirectionalGenomicRegion(
                    "chr"+r[1], r[2].charAt(0), Integer.parseInt(r[3]), Integer.parseInt(r[4])
                    );
            reg.attr= id;
            if(!hm.containsKey(type)){
                hm.put(type, new GenomicRegionsBuilder());
            }
            hm.get(type).add(reg);
            allids.add(id);
        }
    }
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public GenomicRegionsBuilder getOthers(){
    return hm.get(OTHER);
}

public GenomicRegionsBuilder getAll(){
    GenomicRegionsBuilder gb= new GenomicRegionsBuilder();
    gb.addAll(getSUTs());
    gb.addAll(getCUTs());
    gb.addAll(getORFs());
    gb.addAll(getOthers());
    gb.sortAll();
    return gb;
}
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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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  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.a_score.ScoreRNAAnti
  • data.cerevisiae.inhouse.a_score.ScoreRNAGene
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  • data.cerevisiae.inhouse.chip.ChipChipRemoveExtreme
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