Examples of BedExporter

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

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        GenomicRegion gr= it.next();
        if(gr.getValue()==tar){
            gbout.add(gr);
        }
    }
    new BedExporter(gbout).writeToFile(out);
   
   
}
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Examples of fork.lib.bio.anno.genomic.BedExporter

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            gbout.add(gro);
        }
    }
   
public void writeToFile(File out)throws Exception{
    new BedExporter(gbout).writeToFile(out);
}
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Examples of fork.lib.bio.anno.genomic.BedExporter

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        }
        mer.sort();
    }
   
    GenomicRegionsBuilder gbout= mer.getMergedGenomicRegionsBuilder();
    new BedExporter(gbout).writeToFile(out);
   
}
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Examples of fork.lib.bio.anno.genomic.BedExporter

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public void writeToFile(File out)throws Exception {
    PeakIdentifier pi= new PeakIdentifier(lb, null);
    pi.param().joinGap=150;
    GenomicRegionsBuilder gb= pi.getPeaks();
    new BedExporter(gb).writeToFile(out);
}
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Examples of fork.lib.bio.anno.genomic.BedExporter

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protected void writeToFile(File out)throws Exception {
    GenomicRegionsComparator comp= new GenomicRegionsComparator(peaks, anno);
    GenomicRegionsBuilder gbout= comp.getNonIntersection();
    new BedExporter(gbout).writeToFile(out);
}
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Examples of fork.lib.bio.anno.genomic.BedExporter

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            System.out.println(f);
            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            mer.mergeNoSort(gb);
        }
        mer.sort();
        new BedExporter(mer.getMergedGenomicRegionsBuilder()).writeToFile(out);
    }
   
   
}
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Examples of fork.lib.bio.anno.genomic.BedExporter

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public void writeToDirectory(File dir, String tag)throws Exception{
    dir.mkdirs();
    new BedExporter(gbfup).writeToFile(new File(dir+"/"+tag+"_five-up_"+side+".bed"));
    new BedExporter(gbfdown).writeToFile(new File(dir+"/"+tag+"_five-down_"+side+".bed"));
    new BedExporter(gbtup).writeToFile(new File(dir+"/"+tag+"_three-up_"+side+".bed"));
    new BedExporter(gbtdown).writeToFile(new File(dir+"/"+tag+"_three-down_"+side+".bed"));
    new BedExporter(gbin).writeToFile(new File(dir+"/"+tag+"_intra_"+side+".bed"));
    new BedExporter(gbout).writeToFile(new File(dir+"/"+tag+"_inter_"+side+".bed"));
}
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Examples of fork.lib.bio.anno.genomic.BedExporter

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        gr.attr= new Object[]{n, nn};
    }
}
   
public void writeToFile(File out) throws Exception{
    BedExporter be= new BedExporter(gb){
        protected String column3(GenomicRegion gr){
            return ((Object[])gr.attr)[0].toString();
        }
        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

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        if(gr.getValue()!=3300){
            gbout.add(gr);
        }
    }
   
    new BedExporter(gbout).writeToFile(new File(d+"/n3300_"+f.getName()));
   
}
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Examples of fork.lib.bio.anno.genomic.BedExporter

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            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){
            return gr.toUCSCFormat();
        }
        protected String column6On(GenomicRegion gr){
            Object[] os= (Object[])gr.attr;
            return (Double)os[1]+"\t"+ (Double)os[2];
        }
    };
    be.param().ifExpanded= true;
    be.writeToFile(out);
}
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