Examples of GenomicRegionsModifier

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

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    return ret;
}
   

public void writeToDirectory(File od, String org) throws Exception{
    GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
    gm.gb.writeToFileBed(new File(od+"/"+org+"_gene_cds_full.bed"));
    gm.getComplementaryStrand().writeToFileBed(new File(od+"/"+org+"_gene_cds-rev_full.bed"));
    gm.getFivePrimeEnds(500, 0).writeToFileBed(new File(od+"/"+org+"_gene_five_500.0.bed"));
    gm.getFivePrimeEnds(0, 500).writeToFileBed(new File(od+"/"+org+"_gene_five_0.500.bed"));
    gm.getFivePrimeEnds(500, 500).writeToFileBed(new File(od+"/"+org+"_gene_five_500.500.bed"));
    new GenomicRegionsModifier(gm.getGenicRegions(1000, 1000)).lengthGreaterThan(100).writeToFileBed(new File(od+"/"+org+"_gene_cds_1000.1000.bed"));
    gm.getThreePrimeEnds(500, 0).writeToFileBed(new File(od+"/"+org+"_gene_three_500.0.bed"));
    gm.getThreePrimeEnds(0, 500).writeToFileBed(new File(od+"/"+org+"_gene_three_0.500.bed"));
    gm.getThreePrimeEnds(500, 500).writeToFileBed(new File(od+"/"+org+"_gene_three_500.500.bed"));
    gm.getAllIntergenicRegions().writeToFileBed(new File(od+"/"+org+"_intergenic_full.bed"));
    new GenomicRegionsModifier(gm.getAllIntergenicRegions()).getGenicRegions(1000, 1000) .writeToFileBed(new File(od+"/"+org+"_intergenic_1000.bed"));
    new GenomicRegionsModifier(gm.getAllIntergenicRegions()).getGenicRegions(5000, 5000) .writeToFileBed(new File(od+"/"+org+"_intergenic_5000.bed"));
}
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsModifier

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    File anno= new File(dir+"/anno/hg19_ensGene_exon.bed");
   
    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];
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsModifier

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    //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<>();
    File[] lfs= d.listFiles();
    fs.addAll(Arrays.asList(lfs));
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsModifier

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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 gb= new BedReader(f).getGenomicRegionsBuilder();
            GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
            gb= gm.getThreePrimeEnds(150, 0); /////////// modify this
            FastaSequenceExtractor fe= new FastaSequenceExtractor(fastaf, gb, null);

            File of= new File(od+"/"+tag+"_"+FileName.getBaseName(f)+".fasta");
            fe.writeToFastaFile(of);
        }
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsModifier

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protected void init(){}
   

public void writeToDirectory(File od, String org) throws Exception{
    GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
    gm.getFivePrimeEnds(200, 200).writeToFileBed(new File(od+"/"+org+"_gene_five_200.200.bed"));
    gm.getGenicRegions(200, 200).writeToFileBed(new File(od+"/"+org+"_gene_cds_200.200.bed"));
    gm.getThreePrimeEnds(200, 200).writeToFileBed(new File(od+"/"+org+"_gene_three_200.200.bed"));
    new GenomicRegionsModifier(gm.getAllIntergenicRegions()).getGenicRegions(200, 200) .writeToFileBed(new File(od+"/"+org+"_intergenic_200.bed"));
   
}
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsModifier

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        //new File(dir+"/other_datasets/ranjan2013_swr1-chip/swr1-chip_htz1d.wig"),
    };
   
    File an= new File(dir+"/anno/xu_2009_orfs.bed");
    GenomicRegionsBuilder gb= new BedReader(an).getGenomicRegionsBuilder();   
    gb= new GenomicRegionsModifier(gb).getFivePrimeEnds(300, 300);
   
    for(int i=0; i<fs.length ; i++){
        File f= fs[i];
        LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsModifier

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

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

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

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    int len= 150;
    int side= 300;
   
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
    gb= gm.getGenicRegions(side, side);
   
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        DirectionalGenomicRegion gr= (DirectionalGenomicRegion)it.next();
        int i=0;
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