Package fork.lib.bio.anno.genomic

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

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    File anno= new File(dir+"/anno/ensGene_hg19_exon.bed");
   
    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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    File[] fs = d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        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");
           
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    File anno= new File(dir+"/anno/ensGene_hg19_exon.bed");
   
    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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        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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    File[] fs = d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        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));
            File odt= new File(od+"/"+FileName.getBaseName(f));
            SplicedRegionsLocator ll= new SplicedRegionsLocator(peaks, sr);
            ll.writeToDir(odt, "locate");
View Full Code Here
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    File od= new File(d+"/novelIntron");

    int side= -1000;

    SplicedBedReader sr= new SplicedBedReader(annof);
    GenomicRegionsBuilder gbin= sr.getAllIntrons();
    GenomicRegionsModifier gmin= new GenomicRegionsModifier(gbin);
    GenomicRegionsBuilder gbinside= gmin.getExtendedRegions(side, side);
    GenomicRegionsBuilder gbex= sr.getAllExons();
    GenomicRegionsModifier gmex= new GenomicRegionsModifier(gbex);
    GenomicRegionsBuilder gbexside= gmex.getExtendedRegions(500, 500);
   
   
    File[] fs= d.listFiles();
View Full Code Here
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Related Classes of fork.lib.bio.anno.genomic.SplicedBedReader

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