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

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

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    File out= new File(d+"/locate_"+FileName.getBaseName(anno)+".bed");
   
    GenomicRegionsBuilder peaks= new BedReader(f).getGenomicRegionsBuilder();
    SplicedBedReader sr= new SplicedBedReader(anno);
   
    SplicedRegionsLocator ll= new SplicedRegionsLocator(peaks, sr);
    ll.writeToFile(out);
   
   
}
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        if(FileName.getExt(f).equals("bed")){
            GenomicRegionsBuilder peaks= new BedReader(f).getGenomicRegionsBuilder();
            SplicedBedReader sr= new SplicedBedReader(anno);

            File od= new File(d+"/locate/"+ FileName.getBaseName(anno)+"/"+FileName.getBaseName(f));
            SplicedRegionsLocator ll= new SplicedRegionsLocator(peaks, sr);
            ll.writeToDir(od, "locate");
           
            File out= new File(od+".bed");
            ll.writeToFile(out);
        }
    }
   
   
   
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    File out= new File(d+"/locate_"+FileName.getBaseName(anno)+".bed");
   
    GenomicRegionsBuilder peaks= new BedReader(f).getGenomicRegionsBuilder();
    SplicedBedReader sr= new SplicedBedReader(anno);
   
    SplicedRegionsLocator ll= new SplicedRegionsLocator(peaks, sr);
    ll.writeToFile(out);
   
   
}
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            GenomicRegionsBuilder peaks= new BedReader(f).getGenomicRegionsBuilder();
            SplicedBedReader sr= new SplicedBedReader(anno);

            File od= new File(d+"/locate/"+ FileName.getBaseName(anno));
            File odt= new File(od+"/"+FileName.getBaseName(f));
            SplicedRegionsLocator ll= new SplicedRegionsLocator(peaks, sr);
            ll.writeToDir(odt, "locate");
            ll.writeToFile(new File(od+"/locate_"+f.getName()));
           
        }
    }
   
   
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        gr.setValue(Double.parseDouble(r.get(3)));
        gb.add(gr);
    }
    gb.sortAll();
   
    SplicedRegionsLocator sl= new SplicedRegionsLocator(gb, new SplicedBedReader(anno));
   
    File od= new File(d+"/locate");
    File out= new File(d+"/"+FileName.getBaseName(f)+"_locate.bed");
    sl.writeToFile(out);
    sl.writeToDir(od, FileName.getBaseName(f));
   
   
   
   
   
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Related Classes of fork.lib.bio.anno.genomic.region.SplicedRegionsLocator

  • data.human.inhouse.chippeak.ap.Locate
  • data.human.inhouse.chippeak.Locate
  • data.human.inhouse.chippeak.LocateEach
  • data.human.statham2014mods.Locate
  • data.human.statham2014mods.processed.BedToLocate
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