Examples of GenomicRegionsModifier

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

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    File rd= new File(dir+"/data/human_magnus/rna/norm");
    File rfor= new File(rd+"/norm_mcf7_rna3_time-"+time+"_hg19_for.wig");
    File rrev= new File(rd+"/norm_mcf7_rna3_time-"+time+"_hg19_rev.wig");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbnew= new GenomicRegionsModifier(gb).setStrand(strand);
   
    LandscapeBuilder lbf= new BedGraphReader(rfor).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(rrev).getLandscapeBuilder();
   
    LandscapeScoringStrand ls= new LandscapeScoringStrand(lbf, lbr, gbnew);
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsModifier

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    File f= new File(d+"/novel_genes.fpkm_tracking.bed");
    File of= new File(d+"/refine-"+ side+"_"+ f.getName() );
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbref= new BedReader(new File(dir+"/anno/hg19_ensGene_exon.bed")).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbrefs= new GenomicRegionsModifier(gbref).getExtendedRegions(side, side);
   
   
    GenomicRegionsComparator gc= new GenomicRegionsComparator(gb, gbrefs);
    new BedExporter( gc.getNonIntersection() ).writeToFile(of);
   
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsModifier

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        this.gbtr= gbtr;
    }
   
   
public void writeToDir(File od, String tag)throws Exception{
    GenomicRegionsBuilder gbr= new GenomicRegionsModifier(gbtr).getExtendedRegions(side, side);
    GenomicRegionsComparator gc= new GenomicRegionsComparator(gbpeak, gbr);
    File ofa= new File(od+"/asso-"+side+"_"+ tag+".bed");
    File ofn= new File(od+"/asso-not-"+side+"_"+ tag+".bed");
    new BedExporter( gc.getIntersection() ).writeToFile(ofa);
    new BedExporter( gc.getNonIntersection() ).writeToFile(ofn);
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsModifier

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    int side= -1000;

    SplicedBedReader sr= new SplicedBedReader(annof);
    GenomicRegionsBuilder gbin= sr.getAllIntrons();
    GenomicRegionsModifier gmin= new GenomicRegionsModifier(gbin);
    GenomicRegionsBuilder gbinside= gmin.getExtendedRegions(side, side);
    GenomicRegionsBuilder gbex= sr.getAllExons();
    GenomicRegionsModifier gmex= new GenomicRegionsModifier(gbex);
    GenomicRegionsBuilder gbexside= gmex.getExtendedRegions(500, 500);
   
   
    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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protected void init(){}
   

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(300, -150).writeToFileBed(new File(od+"/"+org+"_gene_five_300.-150.bed"));
    gm.getFivePrimeEnds(150, 0).writeToFileBed(new File(od+"/"+org+"_gene_five_150.0.bed"));
    gm.getFivePrimeEnds(0, 150).writeToFileBed(new File(od+"/"+org+"_gene_five_0.150.bed"));
    gm.getFivePrimeEnds(-150, 300).writeToFileBed(new File(od+"/"+org+"_gene_five_-150.300.bed"));
    new GenomicRegionsModifier(gm.getGenicRegions(300, 300)).lengthGreaterThan(100).writeToFileBed(new File(od+"/"+org+"_gene_cds_300.300.bed"));
    gm.getThreePrimeEnds(300, -150).writeToFileBed(new File(od+"/"+org+"_gene_three_300.-150.bed"));
    gm.getThreePrimeEnds(150, 0).writeToFileBed(new File(od+"/"+org+"_gene_three_150.0.bed"));
    gm.getThreePrimeEnds(0, 150).writeToFileBed(new File(od+"/"+org+"_gene_three_0.150.bed"));
    gm.getThreePrimeEnds(-150, 300).writeToFileBed(new File(od+"/"+org+"_gene_three_-150.300.bed"));
    gm.getAllIntergenicRegions().writeToFileBed(new File(od+"/"+org+"_intergenic_full.bed"));
    new GenomicRegionsModifier(gm.getAllIntergenicRegions()).getGenicRegions(300, 300) .writeToFileBed(new File(od+"/"+org+"_intergenic_300.bed"));
   
    gm.getFivePrimeEnds(300, 0).writeToFileBed(new File(od+"/"+org+"_gene_five_300.0.bed"));
    gm.getFivePrimeEnds(0, 300).writeToFileBed(new File(od+"/"+org+"_gene_five_0.300.bed"));
}
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