Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.LandscapeScoringStrand.writeToBedFile()

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        protected double[] scoreStrand(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
            return new double[]{Landscape2DBuffer.getArea(bufs, gr) / (gr.getRange()+1) *1000 };
        }
    };
    File out= new File(od+"/"+tag+"_"+FileName.getBaseName(f)+".bed");
    ls.writeToBedFile(out);

}
   


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    LandscapeBuilder lbf= new BedGraphReader(rfor).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(rrev).getLandscapeBuilder();
   
    LandscapeScoringStrand ls= new LandscapeScoringStrand(lbf, lbr, gbnew);
    ls.writeToBedFile(of);
   
   
   
   
   
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    LandscapeScoringStrand ls= new LandscapeScoringStrand(lbf, lbr, gb){
            protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                return new double[]{Landscape2DBuffer.getArea(bufs, gr) / (gr.getRange()+1)*1000 };
            }
        };
    ls.writeToBedFile(out);
}
   
public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
    File cd= new File(dir+"/data/human_magnus/rna/norm");
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    LandscapeScoringStrand ls= new LandscapeScoringStrand(
            new BarReader(ff).getLandscapeBuilder(),
            new BarReader(fr).getLandscapeBuilder(),
            new BedReader(anno).getGenomicRegionsBuilder()
            );
    ls.writeToBedFile(of);
}
   
   
   
   
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    LandscapeScoringStrand ls= new LandscapeScoringStrand(
            new BarReader(fr).getLandscapeBuilder(),
            new BarReader(ff).getLandscapeBuilder(),
            new BedReader(anno).getGenomicRegionsBuilder()
            );
    ls.writeToBedFile(of);
}
   
   
   
   
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