Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.BedReader

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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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    );
    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();
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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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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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    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();
   
   
   
   
   
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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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    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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public void writeToDir(File od)throws Exception {
    ArrayList<File> fs= GenerateGenic.getFiles();
    for( int i=0; i<fs.size(); i++ ){
        File f= fs.get(i);
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
        LandscapeScoring ls= new LandscapeScoring(lb, gb){
        protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
            return new double[]{Landscape2DBuffer.getArea(bufs, gr) / (gr.getRange()+1) *1000 };
        }

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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()){
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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();
   
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Related Classes of fork.lib.bio.anno.genomic.BedReader

  • data.cerevisiae.at.ATContentBp
  • data.cerevisiae.histmod.kirmizis2009.ProbeMapper$ProbeMapperStrand
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
  • data.cerevisiae.inhouse.a_norm.NormRNASeq
  • data.cerevisiae.inhouse.a_score.ScoreChipGene
  • data.cerevisiae.inhouse.a_score.ScoreChipSeqGene
  • data.cerevisiae.inhouse.a_score.ScoreLen
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.a_score.ScoreRNAAnti
  • data.cerevisiae.inhouse.a_score.ScoreRNAGene
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