Package fork.lib.bio.anno.genomic

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

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        GenomicRegion gr= it.next();
        if(allrs.contains(gr)){
            gr.setValue(1);
        }
    }
    new BedExporter(gb).writeToFile(out);
}
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            }
        }
    }
    BedExporterParam bep= new BedExporterParam();
    bep.ifExpanded=true;
    BedExporter be= new BedExporter(gbout, bep);
    be.writeToFile(out);
}
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                    }
                }
            }

            String tag= "z"+z+"_ac"+ac;
            new BedExporter(gbde).writeToFile(new File(od+"/select-de_"+tag+".bed"));
            GenomicRegionsLocator gl= new GenomicRegionsLocator(
                        gbde,
                        new BedReader(rf).getGenomicRegionsBuilder()
                    );
            gl.writeToSeparateFiles(
                    new File(od+"/locate-de_"+tag+"_in.txt"),
                    new File(od+"/locate-de_"+tag+"_between.txt")
                    );
           
            new BedExporter(gbac).writeToFile(new File(od+"/select-ac_"+tag+".bed"));
            gl= new GenomicRegionsLocator(
                        gbac,
                        new BedReader(rf).getGenomicRegionsBuilder()
                    );
            gl.writeToSeparateFiles(
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}

public void writeToFile(File out)throws Exception{
    BedExporterParam par= new BedExporterParam();
    par.ifExpanded=true;
    BedExporter be= new BedExporter(gb, par){
        protected String column6On(GenomicRegion gr)throws Exception{
            Res r= ress.get(gr);
            return r.str+"\t"+f(r.forl)+"\t"+f(r.forh)+"\t"+f(r.revl)+"\t"+f(r.revh);
        }
        protected double f(double v){
            return (double)Math.round(v*1000)/1000;
        }
    };
    be.writeToFile(out);
}
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    File out= new File("E:\\muxingu\\mystudy\\phd\\files\\anno\\bed\\hg19\\enhancers/human_sorted.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    gb.sortAll();
   
    new BedExporter(gb).writeToFile(out);
   
   
}
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            gbout.add(gr);
        }
    }
    br.close();
   
    new BedExporter(gbout).writeToFile(of);
   
   
}
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        }
    }
    brf.close();
    brr.close();
   
    new BedExporter(gbout).writeToFile(of);
   
   
   
}
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        }
    }
   
   
    File of= new File(od+"/"+FileName.getBaseName(f)+"_cds_"+side+"_"+len+".bed");
    new BedExporter(gbout).writeToFile(of);
}
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    GenomicRegionsBuilder gbref= new BedReader(new File(dir+"/anno/hg19_ensGene_exon.bed")).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbrefs= new GenomicRegionsModifier(gbref).getExtendedRegions(side, side);
   
   
    GenomicRegionsComparator gc= new GenomicRegionsComparator(gb, gbrefs);
    new BedExporter( gc.getNonIntersection() ).writeToFile(of);
   
   
}
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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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