Package fork.lib.bio.anno.genomic

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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    GenomicRegionsComparator comp= new GenomicRegionsComparator(peaks, in);
    GenomicRegionsBuilder gbOverlapIn= comp.getIntersection();
    GenomicRegionsComparator comp2= new GenomicRegionsComparator(gbOverlapIn, ex);
    GenomicRegionsBuilder gbOverlapInNotEx = comp2.getNonIntersection();
   
    new BedExporter(gbOverlapInNotEx).writeToFile(out);
}
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public void writeToDir(File od, String tag)throws Exception{
    GenomicRegionsBuilder gbr= new GenomicRegionsModifier(gbtr).getExtendedRegions(side, side);
    GenomicRegionsComparator gc= new GenomicRegionsComparator(gbpeak, gbr);
    File ofa= new File(od+"/asso-"+side+"_"+ tag+".bed");
    File ofn= new File(od+"/asso-not-"+side+"_"+ tag+".bed");
    new BedExporter( gc.getIntersection() ).writeToFile(ofa);
    new BedExporter( gc.getNonIntersection() ).writeToFile(ofn);
}
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        GenomicRegion gr= it.next();
        Integer len= (int) gr.getRange()+1;
        gr.setValue(len);
    }
   
    new BedExporter(gb).writeToFile(new File(dir+"/anno/bed/"+org+"/prop/"+org+"_length.bed"));
   
}
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    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    gb.removeRedundant();
    gb.sortAll();

   
    new BedExporter(gb).writeToFile(of);
   
   
   
}
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        }
    }
}

public void writeToFile(File out)throws Exception {
    new BedExporter(gbout).writeToFile(out);
}
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            }
        }
    }
    for( int i=0; i<gbouts.size(); i++ ){
        File of= new File(od+"/bin_"+i+".bed");
        new BedExporter(gbouts.get(i)).writeToFile(of);
    }
}
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Related Classes of fork.lib.bio.anno.genomic.BedExporter

  • data.cerevisiae.lee2007.pref.Bin
  • data.cerevisiae.region.aclen.Locate
  • data.cerevisiae.region.GenerateOverviewSet
  • data.cerevisiae.region.GenerateWindowsNonOverlapping
  • data.cerevisiae.region.scan.LinkAntisense
  • data.cerevisiae.region.SortBed
  • data.cerevisiae.region.zpeak.trsc_asso_new.AssoTranscriptionThree
  • data.cerevisiae.region.zpeak.trsc_asso_new.cds.GenerateCDS
  • data.cerevisiae.region.zpeak.trsc_asso_new.Summarise3Anti
  • data.human.inhouse.chippeak.ap.Extract
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