Package fork.lib.bio.anno.genomic

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

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    File anno= new File(dir+"/anno/xu_2009_orfs.bed");
    File forf= new File(rd+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_for.wig");
    File revf= new File(rd+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_rev.wig");
   
   
    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);
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    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){
            protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                return new double[]{Landscape2DBuffer.getArea(bufs, gr) / ((gr.getRange()+1)/1000) / 100 };
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    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();
   
   
    new RandomNew(3044, rd, lbf, lbr, gb);
}
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    while(it.hasNext()){
        String tag= it.next();
        System.out.println(tag);
        File ff= new File(d+"/"+tag+"_for.wig");
        File fr= new File(d+"/"+tag+"_rev.wig");
        LandscapeBuilder lbf= new BedGraphReader(ff).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(fr).getLandscapeBuilder();
        ScoreRNAGene ss= new ScoreRNAGene(lbf, lbr, tag);
        File odt= new File(od+"/"+tag);
        ss.writeToDir(odt);
    }
   
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    File zf= new File(dir+"/anno/bed/sacCer1-xu/cds/xu_2009_orfs_cds_300_150.bed");
    File forf= new File(rd+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_for.wig");
    File revf= new File(rd+"/strand_rna_884-rrp6d_sd_20121119_sacCer1_rev.wig");
   
   
    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);
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    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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    for( int i=0; i<fs.length; i++ ){
    //for( int i=0; i<2; i++ ){
        File f= fs[i];
        System.out.println(f);
        if(FileName.getExt(f).equals("wig")){
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            String tag= FileName.getBaseName(f);
            ScoreChipSeqGene ss= new ScoreChipSeqGene(lb, tag);
            File odt= new File(od+"/"+tag);
            ss.writeToDir(odt);
        }
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}



public void removeShort()throws Exception {
    LandscapeBuilder lb= new BedGraphReader(outSub2).getLandscapeBuilder();
    LandscapeTransformer lt= new LandscapeTransformer(lb);
    lt.selectLength(150, Integer.MAX_VALUE);
    double sum= lb.totalArea();
    double fac= sum/Math.pow(10, 8);
    lt.divideBy( fac );
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    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);
    ls.writeToBedFile(of);
   
   
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    File[] fs= cd.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("wig")){
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            File out= new File(od+"/chip_"+FileName.getBaseName(f)+".bed");
            ScoreMergeChipAbs ss= new ScoreMergeChipAbs(gb, lb);
            ss.writeToFile(out);
        }
    }
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Related Classes of fork.lib.bio.anno.genomic.BedGraphReader

  • data.cerevisiae.auerbach2013_polii.Score
  • data.cerevisiae.histmod.cai2011.Score
  • data.cerevisiae.histmod.guillemett2011_h3k4.Unlog
  • data.cerevisiae.histmod.guillemette2011.Score
  • data.cerevisiae.histmod.kirmizis2009.Score
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
  • data.cerevisiae.histmod.liu2005_histmods.Score
  • data.cerevisiae.histmod.xue2012.Unlog
  • data.cerevisiae.inhouse.a_norm.NormChipChip
  • data.cerevisiae.inhouse.a_norm.NormChipSeqRPM
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