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

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

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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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    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 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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        this.gb=gb;
    }
   
   
public void writeToFile(File out)throws Exception{
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    String[] chrs= gb.getChromosomeList();
    for(int i=0; i<chrs.length ; i++){
        String chr= chrs[i];
        ArrayList<Region> rs= gb.getRegionsForChromosome(chr);
        if(chr.equals("chr10")){
            for(int j=0; j<rs.size() ; j++){
                Region r= rs.get(j);
                if(r.higherThan(117000d)){
                    r.setLowHigh(r.low-310, r.high-310);
                    gbout.add((GenomicRegion)r);
                }else{
                    gbout.add((GenomicRegion)r);
                }
            }
        }else{
            gbout.addAll(chr, rs);
        }
    }
    gbout.writeToFileBed(out);
}
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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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        init();
    }
   

private void init() throws Exception{
    gbout= new GenomicRegionsBuilder();
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        int low = (int)gr.low;
        int high= (int)gr.high;
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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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private void init() throws Exception{
    gb= new GenomicRegionsBuilder();
    ReadTable rt= new ReadTable(f);
    String[][] arr= rt.getTableAsArray();
    for( int i=0; i<arr.length ; i++ ){
        String [] r= arr[i];
        GenomicRegion gr= UCSCRegionParser.parseGenomicRegion(r[4]).getExtendedRegion(-50, -50);
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    File dir = Dirs.getFile("dir");
   
    File d= new File(dir+"/anno\\bed\\sacCer1-xu\\orient");
    File f= new File(d+"/orient3.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        if(gr.getValue()!=3300){
            gbout.add(gr);
        }
    }
   
    new BedExporter(gbout).writeToFile(new File(d+"/n3300_"+f.getName()));
   
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Related Classes of fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder

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  • data.cerevisiae.histmod.kirmizis2009.ProbeMapper$ProbeMapperStrand
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
  • data.cerevisiae.inhouse.a_norm.NormRNASeq
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.a_score.ScoreRNAAnti
  • data.cerevisiae.inhouse.a_score.ScoreRNAGene
  • data.cerevisiae.inhouse.a_score.ScoreRNAGeneRead
  • data.cerevisiae.inhouse.chip.ChipChipRemoveExtreme
  • data.cerevisiae.inhouse.spikein.ScoreSpike
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