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

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

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        String tag = it.next();
        System.out.println(tag);
        String ttag= tag.replace("mcf7_rna3_", "");
       
        File f= new File(d+"/peak_norm_wig_mcf7_chip-h2az_"+ttag+".bed");
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
       
        //System.out.println("xxx"); System.exit(1);
       
        LandscapeBuilder lbf= new BedGraphReader(new File(rnad+"/norm_"+tag+"_for.wig")).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(new File(rnad+"/norm_"+tag+"_rev.wig")).getLandscapeBuilder();
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protected void init() throws Exception{
    gbtel= new BedReader(f).getGenomicRegionsBuilder();
}
   
public void writeToFile(File anno, File out)throws Exception{
    GenomicRegionsBuilder gb= new BedReader(anno).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
   
    String[] chrs= gb.getChromosomeList();
    for(int i=0; i<chrs.length ; i++){
        String chr= chrs[i];
        Region telr= gbtel.getRegionsForChromosome(chr).get(0);
        int low= (int)telr.low+sublen;
        int high= (int)telr.high-sublen;
        Region eur= new Region(low, high);
        ArrayList<Region> rs= gb.getRegionsForChromosome(chr);
        for(int j=0; j<rs.size() ; j++){
            GenomicRegion r= (GenomicRegion)rs.get(j);
            if(eur.contains(r)){
                r.setValue(0);
            }else{
                r.setValue(1);
            }
           
            gbout.add((GenomicRegion)r);
        }
    }
   
    gbout.writeToFileBed(out);
   
}
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public void writeToOutput(File out)throws Exception {
    BedReaderParam brp= new BedReaderParam();
    brp.ifReadExtension=true;
    GenomicRegionsBuilder gb= new BedReader(f, brp).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
   
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        DirectionalGenomicRegion gr= (DirectionalGenomicRegion)it.next();
        String[] ss= ((BedAttribute)gr.attribute()).getOtherFields().get(0).split("/");
        if(ss.length>0){
            boolean ifas= false;
            for( int i=0; i<ss.length; i++ ){
                String s= ss[i];
                if(gr.isOnForwardStrand()){
                    if(s.equals("rev_-")){
                        ifas=true;
                        break;
                    }
                }else{
                    if(s.equals("for_+")){
                        ifas=true;
                        break;
                    }
                }
            }
           
            ((BedAttribute)gr.attribute()).setFieldOther(null);
            if(ifas){
                gr.setValue(-1);
                gbout.add(gr);
            }else{
                gr.setValue(0);
                gbout.add(gr);
            }
        }
    }
    BedExporterParam bep= new BedExporterParam();
    bep.ifExpanded=true;
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    File tarf= new File(dir+"/data\\human_magnus\\h2az\\norm\\peak\\locate\\ensGene_hg19_exon\\peak_norm_wig_mcf7_chip-h2az_time-0_hg19/"+
            "locate_exon.bed");
    File reff= new File(dir+"/anno/bed/hg19/enhancers/human_sorted.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 fa= new File(d+"/score_norm_htz1_len_150.bed");
            File fb= new File(d+"/score_norm_k8ac_len_150.bed");
            GenomicRegionsBuilder gba= new BedReader(fa).getGenomicRegionsBuilder();
            GenomicRegionsBuilder gbb= new BedReader(fb).getGenomicRegionsBuilder();

            GenomicRegionsBuilder gbde= new GenomicRegionsBuilder();
            GenomicRegionsBuilder gbac= new GenomicRegionsBuilder();

            Iterator<GenomicRegion> ita= gba.iterator();
            Iterator<GenomicRegion> itb= gbb.iterator();
            while(ita.hasNext()){
                GenomicRegion ra= ita.next();
                GenomicRegion rb= itb.next();
                double va= ra.getValue();
                double vb= rb.getValue();
                if(va>z){
                    rb.setID(Double.toString(va)+"_"+Double.toString(vb));
                    rb.setValue(0);
                    if(vb<ac){
                        gbde.add(rb);
                    }else{
                        gbac.add(rb);
                    }
                }
            }

            String tag= "z"+z+"_ac"+ac;
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    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
    GenomicRegionsBuilder gb= new GenomicRegionsModifier(new BedReader(anno).getGenomicRegionsBuilder()).getThreePrimeEnds(150, 0);
   
   
    AssoTranscriptionThree ass= new AssoTranscriptionThree(gb, lbf, lbr);
   
    File out= new File(zd+"/asso-trsc_"+anno.getName());
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    File dir= Dirs.getFile("dir");
    File d= new File(dir+"/other_datasets/statham2014_mcf7-mods/");
    File f= new File(d+"/GSM1383850_MCF7_NDR.bed");
    File anno= new File(dir+"/anno/ensGene_hg19_exon.bed");
   
    GenomicRegionsBuilder gb= new GenomicRegionsBuilder();
    ReadTable rt= new ReadTable(f);
    Table<String> tab= rt.getTable();
    for( int i=0; i<tab.getRowNumber(); i++ ){
        ArrayList<String> r= tab.getRow(i);
        DirectionalGenomicRegion gr= new DirectionalGenomicRegion(
                r.get(0),
                '+',
                Integer.parseInt(r.get(1)),
                Integer.parseInt(r.get(2))
        );
        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");
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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);
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    File dir= Dirs.getFile("dir");
    File zd= new File(dir+"/data/chip-seq/norm/peak_new/cds");
    File rf= new File(dir+"/anno/bed/sacCer1-xu/cds/xu_2009_orfs_cds_300_150.bed");
    File datd= new File(dir+"/data/chip-seq/norm");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    LandscapeBuilder lb= new BedGraphReader(new File(datd+"/norm_wig_chip_htz1-anti660_772-wt_sd_20131104-r1_pe1_sacCer1.wig")).getLandscapeBuilder();
   
   
    LandscapeScoring ls= new LandscapeScoring(lb, gb){
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public static void main(String[] args) throws Exception { //debug
    File f= new File("E:\\muxingu\\mystudy\\phd\\files\\anno\\bed\\hg19\\enhancers/human_unsort.bed");
    File out= new File("E:\\muxingu\\mystudy\\phd\\files\\anno\\bed\\hg19\\enhancers/human_sorted.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    gb.sortAll();
   
    new BedExporter(gb).writeToFile(out);
   
   
}
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