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

Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder.sortAll()

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    GenomicRegionsBuilder gb= new GenomicRegionsBuilder();
    gb.addAll(getSUTs());
    gb.addAll(getCUTs());
    gb.addAll(getORFs());
    gb.addAll(getOthers());
    gb.sortAll();
    return gb;
}

   
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        ge.attr= new Object[]{o,
            new Double(r.scores[0]), new Double(r.scores[1])
        };
        gbout.add(ge);
    }
    gbout.sortAll();
    BedExporter be= new BedExporter(gbout){
        protected String column3(GenomicRegion gr){
            return ((Object[])gr.attr)[0].toString();
        }
        protected String column4(GenomicRegion gr){
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                Integer.parseInt(r.get(2))
        );
        gr.setValue(Double.parseDouble(r.get(3)));
        gb.add(gr);
    }
    gb.sortAll();
   
    SplicedRegionsLocator sl= new SplicedRegionsLocator(gb, new SplicedBedReader(anno));
   
    File od= new File(d+"/locate");
    File out= new File(d+"/"+FileName.getBaseName(f)+"_locate.bed");
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public static void main(String[] args) throws Exception { //debug
    File f= new File("E:\\muxingu\\mystudy\\phd\\files\\anno\\bed\\hg19\\enhancers/human_unsort.bed");
    File out= new File("E:\\muxingu\\mystudy\\phd\\files\\anno\\bed\\hg19\\enhancers/human_sorted.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    gb.sortAll();
   
    new BedExporter(gb).writeToFile(out);
   
   
}
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        }else{
            xxx.add(gr);
        }
    }
   
    gbout.sortAll();
    xxx.sortAll();
    return gbout;
}
   
   
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    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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