Package fork.lib.bio.anno.genomic.region

Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsComparator

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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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    }
   
   
   
public void writeToFile(File out)throws Exception {
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(gb, gbcomp).getCrossover();
    HashSet<GenomicRegion> allrs= new HashSet<>();
    Iterator<GenomicRegion> it= gc.both.iterator();
    while(it.hasNext()){
        allrs.add( it.next() );
    }
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    GenomicRegionsBuilder gbc= new BedReader(reff).getGenomicRegionsBuilder();
   
    System.out.println(gbe.size());
    System.out.println(gbc.size());
   
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(gbe, gbc).getCrossover();
    gc.print();

}
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    GenomicRegionsBuilder gbc= new BedReader(reff).getGenomicRegionsBuilder();
   
    System.out.println(gbe.size());
    System.out.println(gbc.size());
   
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(gbe, gbc).getCrossover();
    gc.print();

}
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    random();
}


protected int ovl(GenomicRegionsBuilder tar, GenomicRegionsBuilder ref) throws Exception{
    GenomicRegionsCrossover gc=  new GenomicRegionsComparator(tar, ref).getCrossover();
    //gc.both.print();
    return gc.both.size();
    //return gc.tarOnly.size();
}
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public static GenomicRegionsBuilder overlap(GenomicRegionsBuilder tar, GenomicRegionsBuilder ref)throws Exception {
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(tar, ref).getCrossover();
    return gc.both;
}
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    GenomicRegionsCrossover gc= new GenomicRegionsComparator(tar, ref).getCrossover();
    return gc.both;
}

public static GenomicRegionsBuilder tarOnly(GenomicRegionsBuilder tar, GenomicRegionsBuilder ref)throws Exception {
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(tar, ref).getCrossover();
    return gc.tarOnly;
}
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    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    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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    }
   
   
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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protected void writeToFile(File out)throws Exception {
    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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