Package fork.lib.bio.anno.genomic

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

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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("wig")){
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            int rlen= 100;
            File od= new File(d+"/score/"+FileName.getBaseName(f));
            ScoreChipSeqGene sc= new ScoreChipSeqGene(lb, org, rlen, od, FileName.getBaseName(f));
        }
    }
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    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();

       
        File out= new File("out/line5_"+FileName.getBaseName(f)+".txt");

       
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    //for( int i=0; i<1 ; i++ ){
    for( int i=0; i<fs.length ; i++ ){
        String fn= fs[i];
        File f= new File(wd+"/"+fn+".wig");

        LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
        normalise(lb, new File(od+"/norm_"+f.getName()), "norm_"+fn);
    }
}
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    String samp= "742";
   
   
    File datf= new File(dir+"/data/chip-seq/norm/norm_"+samp+".wig");
    LandscapeBuffer lb= new BedGraphReader(datf).getLandscapeBuilder();
   
   
   
    AntisenseFraction aa= new AntisenseFraction(f, lb);
   
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    for( int i=0; i<samps.length ; i++ ){
    //for( int i=0; i<1 ; i++ ){
        String samp= samps[i];
        LandscapeBuilder lbf= new BedGraphReader(new File(datd+"/strand_rna_"+samp+"_ercc-rna_for.wig")).getLandscapeBuilder();
       
        int rlen= StatRetriever.getReadLen("rna_"+samp)-1;
      
       
       
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        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);
        ss.writeToFile(out);

    }
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public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
    File rnad= new File(dir+"/data/rna-seq");
    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");
    LandscapeBuilder lbf= new BedGraphReader(forf).getLandscapeBuilder();
    LandscapeBuilder lbr= new BedGraphReader(revf).getLandscapeBuilder();
   
    File f= new File("E:\\muxingu\\mystudy\\phd\\files\\data\\chip-seq\\norm\\peak_new/3anti_asso-trsc_xu_2009_orfs.bed");
    //File f= new File("E:\\muxingu\\mystudy\\phd\\files\\data\\chip-seq\\norm\\peak_new\\rand\\three\\runs\\0/anit.bed");
   
    new Fuck2(f, lbf, lbr);
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    //File lbf= new File("/home/forksapien/mystudy/phd/files/data/chip-seq/norm/norm_743.wig");
    //File lbf= new File("/home/forksapien/mystudy/phd/files/data/chip-seq/norm/norm_744.wig");
   
   
    LandscapeScoring ls= new LandscapeScoring(
            new BedGraphReader(lbf).getLandscapeBuilder(),
            new BedReader(reg).getGenomicRegionsBuilder()
            );
   
    File out = new File(d+"/score/score_"+ FileName.getBaseName(lbf)+"_"+FileName.getBaseName(reg)+".bed");
    ls.writeToBedFile(out);
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        File f= new File(d+"/peak_norm_wig_mcf7_chip-h2az_"+ttag+".bed");
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
       
        //System.out.println("xxx"); System.exit(1);
       
        LandscapeBuilder lbf= new BedGraphReader(new File(rnad+"/norm_"+tag+"_for.wig")).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(new File(rnad+"/norm_"+tag+"_rev.wig")).getLandscapeBuilder();
       
        File od= new File(d+"/scoreRNAEach");
        File outf= new File(od+"/score_"+tag+"_for.bed");
        File outr= new File(od+"/score_"+tag+"_rev.bed");
       
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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("wig")){
            data.human.inhouse.chippeak.GetPeaks gg= new data.human.inhouse.chippeak.GetPeaks(new BedGraphReader(f).getLandscapeBuilder());

            File out= new File(od+"/peak_"+FileName.getBaseName(f)+".bed");
            gg.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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