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

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

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    GenomicRegionsBuilder gb= new BedReader(file).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbc= new BedReader(chr).getGenomicRegionsBuilder();
    HashMap<String, GenomicRegion> cr= new HashMap<>();
    Iterator<GenomicRegion> it= gbc.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        cr.put(gr.chr, gr);
    }
    it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        GenomicRegion chrr= cr.get(gr.chr);
        if(chrr!=null){
            double dl= Math.abs(gr.low - chrr.low);
            double dh= Math.abs(gr.high - chrr.high);
            double d= Math.min(dl, dh);
            if(d<thr){
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public void writeToFile(File out) throws Exception{
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    for( int i=0; i<ress.size() ; i++ ){
        LandscapeScoringResultEntry r=ress.get(i);
        GenomicRegion ge= r.gr;
        Object o= ge.attr==null ? ge.toUCSCFormat() : ge.attr;
        ge.attr= new Object[]{o,
            new Double(r.scores[0]), new Double(r.scores[1])
        };
        gbout.add(ge);
    }
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    while(it.hasNext()){
        allrs.add( it.next() );
    }
    it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        if(allrs.contains(gr)){
            gr.setValue(1);
        }
    }
    new BedExporter(gb).writeToFile(out);
}
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                Landscape2DBuffer tsr= new Landscape2DBuffer(lbr.getLandscape2DForChromosome(chr));
               
               
                ArrayList<Region> regs= gb.getRegionsForChromosome(chr);
                for( int j=0; j<regs.size() ; j++ ){
                    GenomicRegion gr= (GenomicRegion)regs.get(j);
                    GenomicRegion grlow, grhigh;
                    int low, high;
                    low= (int)gr.low;
                    high= (int)gr.high;
                    grlow= new GenomicRegion(gr.chr, low-side, low+side);
                    grhigh= new GenomicRegion(gr.chr, high-side, high+side);

                   
                    double forl= score(tsf.reloadAndGetList(grlow), grlow);
                    double forh= score(tsf.reloadAndGetList(grhigh), grhigh);
                    double revl= score(tsr.reloadAndGetList(grlow), grlow);
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        int low= (int)telr.low+sublen;
        int high= (int)telr.high-sublen;
        Region eur= new Region(low, high);
        ArrayList<Region> rs= gb.getRegionsForChromosome(chr);
        for(int j=0; j<rs.size() ; j++){
            GenomicRegion r= (GenomicRegion)rs.get(j);
            if(eur.contains(r)){
                r.setValue(0);
            }else{
                r.setValue(1);
            }
           
            gbout.add((GenomicRegion)r);
        }
    }
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            GenomicRegionsBuilder gbac= new GenomicRegionsBuilder();

            Iterator<GenomicRegion> ita= gba.iterator();
            Iterator<GenomicRegion> itb= gbb.iterator();
            while(ita.hasNext()){
                GenomicRegion ra= ita.next();
                GenomicRegion rb= itb.next();
                double va= ra.getValue();
                double vb= rb.getValue();
                if(va>z){
                    rb.setID(Double.toString(va)+"_"+Double.toString(vb));
                    rb.setValue(0);
                    if(vb<ac){
                        gbde.add(rb);
                    }else{
                        gbac.add(rb);
                    }
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            tsf.keepLeft= 500;
            tsr.keepLeft= 500;
           
            ArrayList<Region> regs= gb.getRegionsForChromosome(chr);
            for( int j=0; j<regs.size() ; j++ ){
                GenomicRegion gr= (GenomicRegion)regs.get(j);
                GenomicRegion grlow, grhigh;
                int low, high;
                low= (int)gr.low;
                high= (int)gr.high;
                grlow= new GenomicRegion(gr.chr, low-side, low+side);
                grhigh= new GenomicRegion(gr.chr, high-side, high+side);
               
                double forl= score(tsf.reloadAndGetList(grlow), grlow);
                double forh= score(tsf.reloadAndGetList(grhigh), grhigh);
                double revl= score(tsr.reloadAndGetList(grlow), grlow);
                double revh= score(tsr.reloadAndGetList(grhigh), grhigh);
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    while((l=br.readLine())!=null){
        String[] ss= l.split("\t");
        String id= ss[0];
        String loc= ss[6];
        if(id.contains("CUFF")){
            GenomicRegion gr= GenomicRegion.parseGenomicRegoinUCSC(loc);
            gr.setID(id);
            gbout.add(gr);
        }
    }
    br.close();
   
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    ArrayList<GenomicRegion> al= gb.getAllGenomicRegions();
    RandomObject<GenomicRegion> rand= new RandomObject( al, null);
    HashSet<GenomicRegion> set= new HashSet<>();
    while(set.size()<n){
        GenomicRegion reg= rand.randomObject();
        if(!set.contains(reg)){
            set.add(reg);
        }
    }
   
    for( int i=0; i<al.size(); i++ ){
        GenomicRegion gr= al.get(i);
        if(set.contains(gr)){
            gbout.add(gr);
        }else{
            xxx.add(gr);
        }
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            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;
            pc= chr;
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