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

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

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        this.gbtr= gbtr;
    }
   
   
public void writeToDir(File od, String tag)throws Exception{
    GenomicRegionsBuilder gbr= new GenomicRegionsModifier(gbtr).getExtendedRegions(side, side);
    GenomicRegionsComparator gc= new GenomicRegionsComparator(gbpeak, gbr);
    File ofa= new File(od+"/asso-"+side+"_"+ tag+".bed");
    File ofn= new File(od+"/asso-not-"+side+"_"+ tag+".bed");
    new BedExporter( gc.getIntersection() ).writeToFile(ofa);
    new BedExporter( gc.getNonIntersection() ).writeToFile(ofn);
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    File rd= new File(dir+"/data\\human_magnus\\rna\\cuff/time-"+time);
   
    File zf= new File(zd+"/novel_mcf7_chip-h2az_time-"+time+"_peaks.bed");
    File rf= new File(rd+"/novel.bed");
   
    GenomicRegionsBuilder gbz= new BedReader(zf).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbr= new BedReader(rf).getGenomicRegionsBuilder();
   
   
   
    CountAssociated cc= new CountAssociated(gbz, gbr);
    cc.writeToDir(rd, FileName.getBaseName(zf));
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        this.probe=probe;
        this.std=std;
        init();
    }
protected void init() throws Exception{
    GenomicRegionsBuilder gba= new BedReader(anno).getGenomicRegionsBuilder();
    String[][] arr= new ReadTable(probe).getTableAsArray();
    double pp=-1; String pc="", pid=""; int ind=0;
    for(int i=0; i<arr.length ; i++){
        String[] r= arr[i];
        if(r[2].equalsIgnoreCase(std)){
            String id= r[0];
            double loc= Double.parseDouble(r[3]);
            String chr= r[1].substring(0,r[1].length()-12).toLowerCase();
            if(ind!=0){
                if(gba.containsChromosome(pc)){
                    if(pc.equals(chr)){
                        GenomicRegion gr= new GenomicRegion(pc, (int)pp, (int)loc-1);
                        ptr.put(pid, gr);
                    }else{
                        double cl= gba.getRegionsForChromosome(pc).get(0).high;
                        GenomicRegion gr= new GenomicRegion(pc, (int)pp, (int)cl-1);
                        ptr.put(pid, gr);
                    }
                }
            }
            if(i==arr.length-1){
                if(gba.containsChromosome(chr)){
                    double cl= gba.getRegionsForChromosome(chr).get(0).high;
                    GenomicRegion gr= new GenomicRegion(chr, (int)loc, (int)cl-1);
                    ptr.put(id, gr);
                }
            }
            pp= loc;
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    double sum= 0;
    for( int i=0; i<fs.length ; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("bed")){
            gfs.add(f);
            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            LandscapeScoring ls= new LandscapeScoring(lb, gb){
                protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                    return new double[]{Landscape2DBuffer.getArea(bufs, gr), gr.getRange()+1 };
                }
            };
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    File cd= new File(dir+"/data/human_magnus/rna/norm");
    File d= new File(dir+"/data\\human_magnus\\h2az\\norm\\peak/merge");
    File od= new File(d+"/scoreRNA");
    File rf= new File(d+"/merge.bed");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    File[] fs= cd.listFiles();
    HashSet<String> tags= new HashSet<>();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
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    //File f= new File(dir+"/anno/sgdGene_sacCer1.bed"); String org= "sacCer1";
    File f= new File(dir+"/anno/xu_2009_orfs.bed"); String org= "sacCer1-xu";
   
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    Iterator<GenomicRegion> it = gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        Integer len= (int) gr.getRange()+1;
        gr.setValue(len);
    }
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    File dir= Dirs.getFile("dir");
   
    File f= new File(dir+"/anno/raw/refGene_hg19_raw.bed");
    File of= new File(dir+"/anno/refGene_hg19.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    gb.removeRedundant();
    gb.sortAll();

   
    new BedExporter(gb).writeToFile(of);
   
   
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        init();
    }
   

protected 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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        init();
    }
   
   
protected void init() throws Exception{
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    FastaSequenceExtractor se= new FastaSequenceExtractor(sf, gb);
    SequenceExtractorEntry en;
    while((en=se.nextEntry())!=null){
        GenomicRegion reg= en.getGenomicRegion();
        String seq= en.getSequence();
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        "1054-wt-gdna_sd-ura_20140313-r2_pe1"
    };
   
    File outd= new File(datd+"/score/"+ty);
   
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();
   
       
    for( int i=0; i<samps.length ; i++ ){
    //for( int i=0; i<1 ; i++ ){
        String samp= samps[i];
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