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

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

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    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);
    }
   
    new BedExporter(gb).writeToFile(new File(dir+"/anno/bed/"+org+"/prop/"+org+"_length.bed"));
   
}
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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;
        int ind= low;
        while( (ind+len)<=high ){
            gbout.add(new GenomicRegion(gr.chr, ind, ind+len-1));
            ind+= len;
        }
    }
}
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    BedGraphExporter.writeTitle(bw, tit);
   
    FastaSequenceExtractor se= new FastaSequenceExtractor(gen, gbout);
    SequenceExtractorEntry en;
    while( (en= se.nextEntry())!=null ){
        GenomicRegion gr= en.getGenomicRegion();
        NucleotideSequence seq= NucleotideSequenceParser.parseSequence(en.getSequence());
        double at= seq.atContent();
        bw.write( gr.toBedFormat()+"\t"+ ((double)Math.round(at*100)/100)+"\n" );
    }
   
    bw.close();
}
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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();
        String id= reg.getID();
        idseq.put(id , seq);
        tab.appendEmptyRow(id);
    }
}
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        String chr= chrs[i];
        Region r= gb.getRegionsForChromosome(chr).get(0);
        double low = r.low;
        while(low+len< r.high){
            Region win= new Region((double)low, (double)low+len-1);
            gbout.add(new GenomicRegion(chr, win));
            low+=len;
        }
    }
}
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protected void init() throws Exception {
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        double v= gr.getValue();
        dis.add(v);
    }
}
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    for( int i=0; i<binn; i++ ){
        gbouts.add(new GenomicRegionsBuilder());
    }
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        double v= gr.getValue() ;
        for( int i=0; i<bs.size()-1; i++ ){
            if( v>=bs.get(i) && v<bs.get(i+1) ){
                gbouts.get(i).add(gr);
                break;
            }
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Related Classes of fork.lib.bio.anno.genomic.region.GenomicRegion

  • data.cerevisiae.at.ATContentBp
  • data.cerevisiae.histmod.kirmizis2009.ProbeMapper$ProbeMapperStrand
  • data.cerevisiae.histmod.magraner2014_histmods.ProcessData
  • data.cerevisiae.lee2007.pref.Bin
  • data.cerevisiae.lee2007.pref.ToSeq
  • data.cerevisiae.region.aclen.Locate
  • data.cerevisiae.region.GenerateOverviewSet
  • data.cerevisiae.region.GenerateWindowsNonOverlapping
  • data.cerevisiae.region.scan.AntisenseFraction
  • data.cerevisiae.region.scan.LinkAntisense
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