Package fork.lib.bio.anno.genomic

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

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    LandscapeScoring ls= new LandscapeScoring(lb, 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 od= new File(dir+"/data/human_magnus/h2az/norm/peak/novel/scoreChip");
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    LandscapeScoring ls= new LandscapeScoring(lb, 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\\h2az\\norm");
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    LandscapeScoring ls= new LandscapeScoring(lb, 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\\h2az\\norm");
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            new BedGraphReader(lbf).getLandscapeBuilder(),
            new BedReader(reg).getGenomicRegionsBuilder()
            );
   
    File out = new File(d+"/score/score_"+ FileName.getBaseName(lbf)+"_"+FileName.getBaseName(reg)+".bed");
    ls.writeToBedFile(out);
   
}
   
   
   
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                return new double[]{Landscape2DBuffer.getArea(bufs, gr) / ((gr.getRange()+1)/1000) / 100 };
            }
        };
   
   
    ls.writeToBedFile(new File(zd+"/score_"+FileName.getBaseName(rf)+".bed") );

}
   
   
}
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            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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    LandscapeScoring ls= new LandscapeScoring(lb, gb){
            protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                return new double[]{Landscape2DBuffer.getArea(bufs, gr)  };
            }
        };
    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\\h2az\\norm");
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                    return new double[]{Landscape2DBuffer.getArea(bufs, gr)  / (gr.getRange()+1)
                    };
                }

            };
            ls.writeToBedFile(new File(od+"/score-lambda_"+FileName.getBaseName(f)+".bed"));
        }
    }
   
   
   
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public void writeToFile(File out)throws Exception {
    File dir= Dirs.getFile("dir");
    File anno= new File(dir+"/anno/bed/sacCer1-xu/sacCer1-xu_gene_five_0.150.bed");
    GenomicRegionsBuilder gb= new BedReader(anno).getGenomicRegionsBuilder();
    LandscapeScoring ls= new LandscapeScoring(lb ,gb);
    ls.writeToBedFile(out);
}
   
   
   
public static void main(String[] args) throws Exception { //debug
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                new BedReader(reg).getGenomicRegionsBuilder()
                );

            File out = new File(outd+"/"+tag+"/set/score-len_"+ FileName.getBaseName(datf)+"_"+FileName.getBaseName(reg)+".bed");
            System.out.println(out);
            ls.writeToBedFile(out);
        }

    }
   
   
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