Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.LandscapeScoring

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    }
   
   
   
public void writeToFile(File out)throws Exception {
    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);
}
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    File lbf= new File("/home/forksapien/mystudy/phd/files/data/chip-seq/norm/norm_742.wig");
    //File lbf= new File("/home/forksapien/mystudy/phd/files/data/chip-seq/norm/norm_743.wig");
    //File lbf= new File("/home/forksapien/mystudy/phd/files/data/chip-seq/norm/norm_744.wig");
   
   
    LandscapeScoring ls= new LandscapeScoring(
            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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    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    LandscapeBuilder lb= new BedGraphReader(new File(datd+"/norm_wig_chip_htz1-anti660_772-wt_sd_20131104-r1_pe1_sacCer1.wig")).getLandscapeBuilder();
   
   
    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) / 100 };
            }
        };
   
   
    ls.writeToBedFile(new File(zd+"/score_"+FileName.getBaseName(rf)+".bed") );

}
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public void writeToDir(File od)throws Exception {
    ArrayList<File> fs= GenerateGenic.getFiles();
    for( int i=0; i<fs.size(); i++ ){
        File f= fs.get(i);
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
        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 };
        }

        };
        File out= new File(od+"/"+tag+"_"+FileName.getBaseName(f)+".bed");
        ls.writeToBedFile(out);
    }
}
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    }
   
   
   
public void writeToFile(File out)throws Exception {
    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);
}
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    for( int i=0; i<fs.length ; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("bed")){
            gfs.add(f);
            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            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 };
                }
            };
            Distribution dis= LandscapeScoringResultEntry.toDistribution(ls.getResultEntries(), 0);
            lens.add(LandscapeScoringResultEntry.toDistribution(ls.getResultEntries(), 1).sum());
            double s= dis.sum();
            vs.add(s); sum+=s;
            //LandscapeScoringResultEntry.writeToFile(ls.getResultEntries(), new File(out.getParentFile()+"/file_"+f.getName()) );
        }
    }
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    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("wig")){
            System.out.println(f);
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            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)
                    };
                }

            };
            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);
}
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            String samp= samps[k];
            String tag= samp+"_"+rep;
            File datf= new File(datd+"/norm_wig_chip_"+samp+"_"+rep+"_sacCer1.wig");
            //File datf= new File(datd+"/norm_"+samp+".wig");

            LandscapeScoring ls= new LandscapeScoring(
                new BedGraphReader(datf).getLandscapeBuilder(),
                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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    od.mkdirs();
    File[] fs= files(org);
    for(int i=0; i<fs.length ; i++){
        File f=fs[i];
        System.out.println(f);
        ls= new LandscapeScoring(lb, new BedReader(f).getGenomicRegionsBuilder()){
            protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                return new double[]{Landscape2DBuffer.getArea(bufs, gr) /100 / ((gr.getRange()+1)/1000) };
            }
        };
        File out= new File(od+"/"+samp+"_"+FileName.getBaseName(f)+".bed");
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Related Classes of fork.lib.bio.anno.genomic.LandscapeScoring

  • data.cerevisiae.inhouse.a_score.ScoreChipGene
  • data.cerevisiae.inhouse.a_score.ScoreChipSeqGene
  • data.cerevisiae.inhouse.a_score.ScoreLen
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.spikein.ScoreSpike
  • data.cerevisiae.lee2007.pref.ScoreWindow
  • data.cerevisiae.region.scan.AntisenseFraction
  • data.cerevisiae.region.scan.ScanIntra
  • data.cerevisiae.region.wt4krlen.ScoreLen
  • data.cerevisiae.region.zpeak.trsc_asso_new.cds.Score
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