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

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

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    );
    File reff= new File(d2+"/peak_norm_wig_mcf7_chip-h2az_time-0_hg19"+
            "/locate_intergenic.bed"
    );
   
    GenomicRegionsBuilder gbe= new BedReader(tarf).getGenomicRegionsBuilder();
    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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    File d= new File(dir+"/data/human_magnus/rna/cuff/time-5");
   
    File f= new File(d+"/genes.fpkm_tracking");
    File of= new File(d+"/novel_"+f.getName()+".bed");
   
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    BufferedReader br= new BufferedReader(new FileReader(f));
    String l;
    while((l=br.readLine())!=null){
        String[] ss= l.split("\t");
        String id= ss[0];
        String loc= ss[6];
        if(id.contains("CUFF")){
            GenomicRegion gr= GenomicRegion.parseGenomicRegoinUCSC(loc);
            gr.setID(id);
            gbout.add(gr);
        }
    }
    br.close();
   
    new BedExporter(gbout).writeToFile(of);
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    File forf= new File(rnad+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_for.wig");
    File revf= new File(rnad+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_rev.wig");
   
    File rd= new File(dir+"/data/chip-seq/norm/peak_new/rand/cds");
   
    GenomicRegionsBuilder gb= new BedReader(new File(dir+"/anno/bed/sacCer1-xu/cds/xu_2009_orfs_cds_300_150.bed")).getGenomicRegionsBuilder();
   
    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
   
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    //for( int i=0; i<100; i++ ){
    for( int i=0; i<1; i++ ){
        FrequencyCount<Integer> lens= gbtar.lengthDistribution();
        //System.out.print(i+"    ");
       
        GenomicRegionsBuilder rset= new RandomGenomicRegionSet(gball, lens).getRandomGenomicRegions();
        //rset.print();
       
        int ovl= ovl(rset, gbref);
        System.out.println(rset.size()+"   "+  gbref.size()+"   "+ovl);
       
    }
}
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    File xf= new File(dir+"/data/human_magnus/"+xxx+"/norm/peak/locate/ensGene_hg19_exon"+
            "/peak_norm_wig_mcf7_chip-"+xxx+"_time-0_hg19"+
            "/locate_"+pos+".bed"
    );
   
    GenomicRegionsBuilder gbe= new BedReader(ef).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbem= new BedReader(emf).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbz= new BedReader(zf).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbx= new BedReader(xf).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbinter= new BedReader(af).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbndr= new BedReader(new File(dir+"/other_datasets/statham2014_mcf7-mods/locate/GSM1383850_MCF7_NDR_"+pos+".bed")).getGenomicRegionsBuilder();
   
   
   
   
   
    GenomicRegionsBuilder gba= overlap(gbem, gbz);
    GenomicRegionsBuilder gbb= gbndr;  

    System.out.println("a: "+gba.size());
    System.out.println("b: "+gbb.size());
    InspectCrossover ins = new InspectCrossover(gba, gbb, gbinter );
   
   
   
   
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public void writeToDir(File od)throws Exception {
    File dir= Dirs.getFile("dir");
    File f= new File(dir+"\\anno\\bed\\hg19\\refGene_hg19\\genic\\hg19_gene_five_0.500.bed");
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    LandscapeScoringStrand ls= new LandscapeScoringStrand(lbf , lbr, gb){
        @Override
        protected double[] scoreStrand(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
            return new double[]{Landscape2DBuffer.getArea(bufs, gr) / (gr.getRange()+1) *1000 };
        }
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    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
    GenomicRegionsBuilder gb= new BedReader(zf).getGenomicRegionsBuilder();
   
   
    AssoTranscriptionThree ass= new AssoTranscriptionThree(gb, lbf, lbr);
   
    File out= new File(zd+"/asso-trsc_"+zf.getName());
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    BufferedWriter bw= new BufferedWriter(new FileWriter(out));
    for( int i=0; i<1000; i++ ){
        System.out.println(i);
        File od= new File(rundir+"/"+i);
        od.mkdirs();
        GenomicRegionsBuilder gbout= generateRegions();
       
        AssoTranscriptionThree ass= new AssoTranscriptionThree(gbout, lbf, lbr);
        File asso= new File(od+"/asso.bed");
        ass.writeToFile(asso);
        Summarise3Anti ss= new Summarise3Anti(asso);
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GenomicRegionsBuilder xxx;
protected GenomicRegionsBuilder generateRegions() throws Exception{
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    xxx= new GenomicRegionsBuilder();
   
    ArrayList<GenomicRegion> al= gb.getAllGenomicRegions();
    RandomObject<GenomicRegion> rand= new RandomObject( al, null);
    HashSet<GenomicRegion> set= new HashSet<>();
    while(set.size()<n){
        GenomicRegion reg= rand.randomObject();
        if(!set.contains(reg)){
            set.add(reg);
        }
    }
   
    for( int i=0; i<al.size(); i++ ){
        GenomicRegion gr= al.get(i);
        if(set.contains(gr)){
            gbout.add(gr);
        }else{
            xxx.add(gr);
        }
    }
   
    gbout.sortAll();
    xxx.sortAll();
    return gbout;
}
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    File forf= new File(rnad+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_for.wig");
    File revf= new File(rnad+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_rev.wig");
   
    File rd= new File(dir+"/data/chip-seq/norm/peak_new/rand/three");
   
    GenomicRegionsBuilder gb= new GenomicRegionsModifier(new BedReader(anno).getGenomicRegionsBuilder()).getThreePrimeEnds(150, 0);
   
    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
    new RandomNew(927, rd, lbf, lbr, gb);
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