Examples of writeToFile()

Examples of data.human.test.trsc.ScoreMergeAgainstRNA.writeToFile()

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        ScoreMergeAgainstRNA ss= new ScoreMergeAgainstRNA(gb, lbf, lbr);
        ss.writeToFile(outf);
       
        ss= new ScoreMergeAgainstRNA(gb, lbr, lbf);
        ss.writeToFile(outr);
       
    }
   
   
   
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Examples of fork.lib.bio.anno.genomic.BedExporter.writeToFile()

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        }
        protected String column4(GenomicRegion gr){
            return ((Object[])gr.attr)[1].toString();
        }
    };
    be.writeToFile(out);
}
   
   

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Examples of fork.lib.bio.anno.genomic.BedExporter.writeToFile()

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            Object[] os= (Object[])gr.attr;
            return (Double)os[1]+"\t"+ (Double)os[2];
        }
    };
    be.param().ifExpanded= true;
    be.writeToFile(out);
}



public static void main(String[] args) throws Exception {
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Examples of fork.lib.bio.anno.genomic.BedExporter.writeToFile()

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        }
    }
    BedExporterParam bep= new BedExporterParam();
    bep.ifExpanded=true;
    BedExporter be= new BedExporter(gbout, bep);
    be.writeToFile(out);
}
   
   
   
   
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Examples of fork.lib.bio.anno.genomic.BedExporter.writeToFile()

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        }
        protected double f(double v){
            return (double)Math.round(v*1000)/1000;
        }
    };
    be.writeToFile(out);
}


protected double score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
    return Landscape2DBuffer.getArea(bufs, gr) / (gr.getRange()+1) ;
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Examples of fork.lib.bio.anno.genomic.BedGraphExporter.writeToFile()

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    }
   
   
    BedGraphExporter be =new BedGraphExporter(lb);
    be.param().tit= FileName.getBaseName(out);
    be.writeToFile(out);
}
   
   
}
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Examples of fork.lib.bio.anno.genomic.BedGraphExporter.writeToFile()

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    Distribution dnz= lb.getDistributionNonZero();
    double nf= dnz.sum()/ 100000000;
    new LandscapeTransformer(lb).divideBy(nf);
    BedGraphExporter be= new BedGraphExporter(lb);
    be.param().tit= tit;
    be.writeToFile(f);
}
   
   
   
   
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Examples of fork.lib.bio.anno.genomic.LandscapeComparatorBuffer.writeToFile()

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            public double newValue(double v, double refv) {
                return new Double( (double)Math.round( (v- refv) * 1000)/1000  );
            }
        };
    String tag= FileName.getBaseName(f);
    lc.writeToFile(out, "diff"+tag);
}


public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsLocator.writeToFile()

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        GenomicRegionsLocator gl= new GenomicRegionsLocator(
                new BedReader(f).getGenomicRegionsBuilder(),
                new BedReader(rf).getGenomicRegionsBuilder()
            );
        File out= new File(od+"/location_"+tt+".bed");
        gl.writeToFile(out);
    }
   
   
   
   
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Examples of fork.lib.bio.anno.genomic.region.SplicedRegionsLocator.writeToFile()

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    GenomicRegionsBuilder peaks= new BedReader(f).getGenomicRegionsBuilder();
    SplicedBedReader sr= new SplicedBedReader(anno);
   
    SplicedRegionsLocator ll= new SplicedRegionsLocator(peaks, sr);
    ll.writeToFile(out);
   
   
}
   
   
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