Package fork.lib.bio.anno.genomic

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

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public void writeToFile(File out)throws Exception{
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder(),
            gbf= new BedReader(fw).getGenomicRegionsBuilder(),
            gbr= new BedReader(ft).getGenomicRegionsBuilder();
    Iterator<GenomicRegion> itw= gbf.iterator();
    Iterator<GenomicRegion> itt= gbr.iterator();
    while(itw.hasNext()){
        GenomicRegion grf= itw.next();
        GenomicRegion grr= itt.next();
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    //File anno= new File(dir+"/anno/refseq_hg19_exon.bed");
    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 f= new File(d+"/locate_ensGene_hg19_exon.bed");
    int tar= 5;
    File out= new File(od+"/"+tar+"_"+FileName.getBaseName(f)+".bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbout = new GenomicRegionsBuilder();
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        if(gr.getValue()==tar){
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    File f= new File(d+"/5_locate_ensGene_hg19_exon.bed");
    File out = new File(d+"/side-right_"+ Integer.toString(side)+"_"+f.getName() );
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    GenerateSideRegion gg= new GenerateSideRegion(gb);
   
    gg.writeToFile(out);
   
   
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    File d= new File(dir+"/data\\human_magnus\\h2az/macs/");
    File od= new File(d+"/scoreNorm");
    File rf= new File(d+"/mcf7_chip-h2az_time-0_peaks.bed");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    File[] fs= cd.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        System.out.println(f);
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    File d= new File(dir+"/data\\human_magnus\\h2az/macs/merge/extract");
    File od= new File(d+"/scoreNorm");
    File rf= new File(d+"/5_locate_ensGene_hg19_exon.bed");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    File[] fs= cd.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        System.out.println(f);
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    File od= new File(d+"/scoreRNA");
   
    File f= new File(d+"/side-right_200_5_locate_ensGene_hg19_exon.bed");
   
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    File[] rfs= rnad.listFiles();
    HashSet<String> tags= new HashSet<>();
    for( int i=0; i<rfs.length; i++ ){
        File rf= rfs[i];
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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") && !f.getName().equals(out.getName()) ){
            System.out.println(f);
            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            mer.mergeNoSort(gb);
        }
        mer.sort();
    }
   
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    File od= new File(dir+"/anno/bed/"+org+"/"+tag+"_"+org+"/genic");
   
    BedReaderParam par= new BedReaderParam();
    par.ifDirectional=true;
   
    GenomicRegionsBuilder gb= new BedReader(f, par).getGenomicRegionsBuilder();
   
    GenerateGenic gg= new GenerateGenic(gb);
    gg.writeToDirectory(od, org);
}
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    File od= new File(d+"/novel");
   
    int side= 5000;
    GenomicRegionsBuilder gbanno= new GenomicRegionsModifier(
            new BedReader(anno).getGenomicRegionsBuilder()).getExtendedRegions(side, side);
   
    File[] fs= d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File pf= fs[i];
        if(FileName.getExt(pf).equals("bed")){
            GenomicRegionsBuilder gbpeak= new BedReader(pf).getGenomicRegionsBuilder();
            GetNovelPeaks gn= new GetNovelPeaks(gbpeak, gbanno);

            File out= new File(od+"/novel_"+ pf.getName());
            gn.writeToFile(out);
        }
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Related Classes of fork.lib.bio.anno.genomic.BedReader

  • data.cerevisiae.at.ATContentBp
  • data.cerevisiae.histmod.kirmizis2009.ProbeMapper$ProbeMapperStrand
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
  • data.cerevisiae.inhouse.a_norm.NormRNASeq
  • data.cerevisiae.inhouse.a_score.ScoreChipGene
  • data.cerevisiae.inhouse.a_score.ScoreChipSeqGene
  • data.cerevisiae.inhouse.a_score.ScoreLen
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.a_score.ScoreRNAAnti
  • data.cerevisiae.inhouse.a_score.ScoreRNAGene
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