Package fork.lib.bio.anno.genomic

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

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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/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 dir= Dirs.getFile("dir");
    File od= new File(dir+"/data/human_magnus/h2az/norm/peak/novel/scoreChip");
    File cd= new File(dir+"\\data\\human_magnus\\h2az\\norm");
    File rf= new File(dir+"/data\\human_magnus\\h2az\\norm\\peak\\novel/merge.bed");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    File[] fs= cd.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("wig")){
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    //File d= new File(dir+"/data\\human_magnus\\h2az\\norm\\peak/merge");
    File d= new File(dir+"/data\\human_magnus\\h2az/macs/merge");
    File od= new File(d+"/scoreNorm");
    File rf= new File(d+"/merge.bed");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    File[] fs= cd.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("wig")){
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public void addMergeFile(File f)throws Exception {
    String cntag= FileName.getBaseName(f);
    HashMap<String, String> hma= new HashMap<>();
    HashMap<String, String> hmb= new HashMap<>();
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        String u= gr.chr+":"+(int)gr.low+"-"+(int)gr.high;
        hma.put( u, gr.getID());
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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();
        new BedExporter(mer.getMergedGenomicRegionsBuilder()).writeToFile(out);
    }
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    double sthr= 0.6;
    double zthr= 80;
    File dir= Dirs.getFile("dir");
   
   
    GenomicRegionsBuilder gbl= new BedReader(new File(dir+"/anno/bed/len/len_150_off_0.bed")).getGenomicRegionsBuilder();
    ArrayList<LandscapeScoringResultEntry> rsz= new LandscapeScoring(
            new BedGraphReader(new File(dir+"/data/chip-seq/norm/norm_wig_chip_742-wt_r1_sacCer1.wig")).getLandscapeBuilder(),
            gbl
            ).getResultEntries();
   
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        String fn= FileName.getBaseName(f);
        if(fn.indexOf("chr")==0){
            chrGet.put(fn, new GetSequenceFasta(f));;
        }
    }
    idReg= new BedReader(bedf).getIDToRegionMap();
}
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    od.mkdirs();
    File[] fs= ScoreChipGene.files("sacCer1-xu");
    for(int i=0; i<fs.length ; i++){
        File f=fs[i];
        System.out.println(f);
        ls= new LandscapeScoring(lb, new BedReader(f).getGenomicRegionsBuilder()){
            protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                return new double[]{Landscape2DBuffer.getArea(bufs, gr)};
            }
        };
        File out= new File(od+"/"+FileName.getBaseName(f)+".bed");
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    File ld= new File(d+"/lineup");
    //File regf= new File(ld+"/chr3_cn3300_cz3.bed");
    File regf= new File(ld+"/chr3_cn3300_cnz3.bed");
   
   
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();
    GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
    gb= gm.getThreePrimeEnds(300, 100);
   
    File od= new File(ld+"/"+FileName.getBaseName(regf));
    ArrayList<File> fs= new ArrayList<>();
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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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