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

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

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    GetSequenceFasta get= new GetSequenceFasta(new File(dir+"/anno/genomes/sacCer1/sacCer1.fa"));
   
    for( int i=0; i<10; i++ ){
        File f= new File(d+"/bin_"+i+".bed");
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
        ToSeq tt= new ToSeq(gb, get);
        File of= new File(od+"/seq_"+FileName.getBaseName(f)+".fasta");
        tt.writeToFile(of);
    }
   
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        "749-htz1oe_ypg_20140313-r2_pe1",
    };
   
    File outd= new File(datd+"/score/");
   
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();
   
       
    for( int i=0; i<samps.length ; i++ ){
    //for( int i=0; i<1 ; i++ ){
        String samp= samps[i];
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        "0"
    };
    for( int i=0; i<ts.length; i++ ){
        String t= ts[i];
        File rf= new File(d+"/peak_norm_wig_mcf7_chip-h2az_time-"+t+"_hg19.bed");
        GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
       
        File f= new File(cd+"/norm_wig_mcf7_chip-h2az_time-"+t+"_hg19.wig");
        LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
        File out= new File(od+"/chip_"+FileName.getBaseName(f)+".bed");
        ScoreChipNormEach ss= new ScoreChipNormEach(gb, lb);
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protected void init() throws Exception{
    hm= new HashSet();
    hmnot= new HashSet();
    GenomicRegionsBuilder gb= new BedReader(file).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbc= new BedReader(chr).getGenomicRegionsBuilder();
    HashMap<String, GenomicRegion> cr= new HashMap<>();
    Iterator<GenomicRegion> it= gbc.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        cr.put(gr.chr, gr);
    }
    it= gb.iterator();
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protected void init() throws Exception{
    ress= new ArrayList<>();
    GenomicRegionsBuilder ggg= new GenomicRegionsModifier(new GenomicRegionsModifier(gb).getComplementaryStrand()).getExtendedRegions(out, out);
   
    LandscapeScoringStrand ls= new LandscapeScoringStrand(lbf, lbr, ggg
            ){
        protected double[] scoreStrand(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
            return Landscape2DBuffer.getLandscape(bufs, gr);
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    File compf= new File(dir+"/other_datasets\\statham2014_mcf7-mods\\norm\\peaks\\locate\\ensGene_hg19_exon/locate_peak_norm_wig_mcf7_h3k4me1_SRR1282220_hg19.bed");
    //File compf= new File(dir+"/other_datasets\\statham2014_mcf7-mods\\norm\\peaks\\locate\\ensGene_hg19_exon/locate_peak_norm_wig_mcf7_h3k27ac_SRR1282218_hg19.bed");
    //File compf= new File(dir+"/other_datasets/statham2014_mcf7-mods/GSM1383850_MCF7_NDR_locate.bed");
   
    GenomicRegionsBuilder gbcomp= new BedReader(compf).getGenomicRegionsBuilder();
   
    String[] ts= new String[]{
        "0"
    };
    for( int i=0; i<ts.length; i++ ){
        String t= ts[i];
        File f= new File(d+"/peak_norm_wig_mcf7_chip-h2az_time-"+t+"_hg19.bed");
       
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
        String tag= FileName.getBaseName(compf);
        LinkChip ll= new LinkChip(gb, gbcomp);
        File out= new File(od+"/"+tag+"/time-"+t+"_"+tag+".bed");
        ll.writeToFile(out);
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public void writeToFile(File out) throws Exception{
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    for( int i=0; i<ress.size() ; i++ ){
        LandscapeScoringResultEntry r=ress.get(i);
        GenomicRegion ge= r.gr;
        Object o= ge.attr==null ? ge.toUCSCFormat() : ge.attr;
        ge.attr= new Object[]{o,
            new Double(r.scores[0]), new Double(r.scores[1])
        };
        gbout.add(ge);
    }
    gbout.sortAll();
    BedExporter be= new BedExporter(gbout){
        protected String column3(GenomicRegion gr){
            return ((Object[])gr.attr)[0].toString();
        }
        protected String column4(GenomicRegion gr){
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protected File f;
protected LandscapeBuilder lbf, lbr;
   
   
    public Fuck2(File f, LandscapeBuilder lbf, LandscapeBuilder lbr)throws Exception {
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
       
        String[] chrs= gb.getUnsortedChromosomeList();
        for( int i=0; i<chrs.length ; i++ ){
            String chr= chrs[i];
            if(lbf.containsChromosome(chr) && lbr.containsChromosome(chr) ){
                Landscape2DBuffer tsf= new Landscape2DBuffer(lbf.getLandscape2DForChromosome(chr));
                Landscape2DBuffer tsr= new Landscape2DBuffer(lbr.getLandscape2DForChromosome(chr));
               
               
                ArrayList<Region> regs= gb.getRegionsForChromosome(chr);
                for( int j=0; j<regs.size() ; j++ ){
                    GenomicRegion gr= (GenomicRegion)regs.get(j);
                    GenomicRegion grlow, grhigh;
                    int low, high;
                    low= (int)gr.low;
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public static void main(String[] args) throws Exception {
    File dir= Dirs.getFile("dir");
    File fd= new File(dir+"/data/rna");
    File f= new File("out/score/set/sacCer1-xu/scan/intra_300_0_10_51.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    String s= "884-rrp6d-wt";
    LandscapeBuffer lbf= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_for.wig"));
    LandscapeBuffer lbr= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_rev.wig"));
    System.out.println(1);
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public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
    File od= new File(dir+"/anno/bed/sacCer1-xu/orient");

    File f= new File(dir+"/anno/xu_2009_orfs.bed");
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
   
    String[] chrs= gb.getChromosomeList();
    for(int i=0; i<chrs.length ; i++){
        String chr= chrs[i];
        ArrayList<Region> regs= gb.getRegionsForChromosome(chr);
        for(int j=0; j<regs.size() ; j++){
            DirectionalGenomicRegion dr= (DirectionalGenomicRegion)regs.get(j);
            if(dr.isOnForwardStrand()){
                if( j== regs.size()-1 ){
                    dr.setValue(331);
                }else{
                    DirectionalGenomicRegion drn= (DirectionalGenomicRegion) regs.get(j+1);
                    if(drn.isOnForwardStrand()){
                        add(dr, drn, "35");
                    }else{
                        add(dr, drn, "33");
                    }
                }
            }else{
                if(j==0){
                    dr.setValue(331);
                }else{
                    DirectionalGenomicRegion drn= (DirectionalGenomicRegion) regs.get(j-1);
                    if(drn.isOnReverseStrand()){
                        add(dr, drn, "35");
                    }else{
                        add(dr, drn, "33");
                    }
                }
            }
            gbout.add(dr);
        }
    }
   
   
   
   
    gbout.writeToFileBed(new File(od+"/orient3.bed"));
   
}
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