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

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

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            gbf= new BedReader(fw).getGenomicRegionsBuilder(),
            gbr= new BedReader(ft).getGenomicRegionsBuilder();
    Iterator<GenomicRegion> itw= gbf.iterator();
    Iterator<GenomicRegion> itt= gbr.iterator();
    while(itw.hasNext()){
        GenomicRegion grf= itw.next();
        GenomicRegion grr= itt.next();
        double vw= grf.getValue();
        double vt= grr.getValue();
        double lfc;
        if(vw<10 & vt<10){
            lfc=0;
        }else{
            double vwm= vw==0 ? 0.1 : vw;
            double vtm= vt==0 ? 0.1 : vt;
            lfc= Math.log(vtm/vwm)/Math.log(2);
        }
        GenomicRegion gr= grf.clone();
        gr.setValue(lfc);
        gbout.add(gr);
    }
    gbout.writeToFileBed(out);
}   
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    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()==tar){
            gbout.add(gr);
        }
    }
    new BedExporter(gbout).writeToFile(out);
   
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    HashMap<String, String> hma= new HashMap<>();
    HashMap<String, String> hmb= new HashMap<>();
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        String u= gr.chr+":"+(int)gr.low+"-"+(int)gr.high;
        hma.put( u, gr.getID());
        hmb.put( u, Double.toString(gr.getValue()));
    }
    this.addHashMapIDToVal(hma, cntag+"_gene");
    this.addHashMapIDToVal(hmb, cntag+"_loc");
}
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    }catch(RegionException re){}
}

protected void addInter(DirectionalGenomicRegion dra, DirectionalGenomicRegion drb){
    try{
        gbout.add(new GenomicRegion(dra.chr, (int)(dra.high+side+1), (int)(drb.low-side-1)));
    }catch(RegionException re){}
}
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    Table<String> tab= rt.getTable();
    for( int i=0; i<tab.getRowNumber(); i++ ){
        ArrayList<String> r= tab.getRow(i);
        String reg= r.get(9);
        if(!reg.equals("")){
            GenomicRegion gr= GenomicRegion.parseGenomicRegoinUCSC(reg);
            idreg.put(r.get(0), gr);
            //System.out.println(r.get(0)+"   "+ gr.toUCSCFormat());
        }
    }
   
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    gb= new BedReader(file).getGenomicRegionsBuilder();
   
    CrossAnno cr= new CrossAnno(link,0,1);
    Iterator<GenomicRegion> it = gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        String n= gr.attr.toString();
        String nn= cr.map(n);
        if(nn==null){
            nn= n;
        }
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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;
        int ind= low+off;
        while( (ind+len)<=high ){
            gbout.add(new GenomicRegion(gr.chr, ind, ind+len-1));
            ind+= len;
        }
    }
}
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    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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    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);
        double vf= Double.parseDouble(r[6]);
        double vt= Double.parseDouble(r[7]);
        double d= vt-vf;
        double rat= vt/vf;
        if(rat>2 && d>7){
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public void writeToFile(File out)throws Exception {
    FastaExporter fe= new FastaExporter(out);
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        String seq= get.getSequence(gr);
        fe.appendEntry(new FastaEntry(gr.toUCSCFormat(), seq));
        String cseq = NucleotideSequenceParser.parseSequence(seq).complementary().toString();
        DirectionalGenomicRegion cgr= new DirectionalGenomicRegion(gr.chr, '-', (int)gr.low, (int)gr.high);
        fe.appendEntry(new FastaEntry( cgr.toUCSCFormat(), cseq));
    }
    fe.close();
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