Package fork.lib.bio.anno.genomic

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

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    //File f= new File(d+"/GSM897361_H3K18_timeA_signal.bar"); String tag= "h3k18ac";
    File f= new File(d+"/GSM897366_H4K16_timeA_signal.bar"); String tag= "h4k16ac";
   
    File od= new File(d+"/score/"+tag);
    LandscapeBuilder lb= new BarReader(f).getLandscapeBuilder();
    ScoreChipGene sc= new ScoreChipGene(lb, org, od, tag+"_xue2012");
   
   
}
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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("bar")){
            LandscapeBuilder lb= new BarReader(f).getLandscapeBuilder();

            File of= new File(d+"/"+FileName.getBaseName(f)+".wig");
            new BedGraphExporter(lb).writeToFile(of);;
        }
    }
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    String org= "refGene_hg19";
    //File f= new File(d+"/H9_H2A.Z.bar");
    File f= new File(d+"/H9_H3K56ac.bar");
    LandscapeBuffer lb= new BarReader(f);
   
   
    File od= new File(d+"/"+FileName.getBaseName(f));
    ScoreChipGene sc= new ScoreChipGene(lb, org, od, FileName.getBaseName(f));
   
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    String org= "sacCer1-xu";
    File f= new File(d+"/unlog_analyzed_data_complete_bw20.bar");
   
   
    LandscapeBuilder lb= new BarReader(f).getLandscapeBuilder();
    ScoreChipGene sc= new ScoreChipGene(lb, org, od, "lee2007");
   
   
   
   
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    String org= "sacCer1-xu";
    File f= new File(d+"/unlog_analyzed_data_complete_bw20.bar");
   
   
    LandscapeBuilder lb= new BarReader(f).getLandscapeBuilder();
    ScoreChipGene sc= new ScoreChipGene(lb, org, od, "lee2007");
   
   
   
   
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        init();
    }
   
   
protected void init() throws Exception{
    lbref= new BarReader(leef).getLandscapeBuilder();
}
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    File dir= Dirs.getFile("dir");
    File d= new File(dir+"/other_datasets/lee_2007");
   
    File f= new File(d+"/analyzed_data_complete_bw20.bar");
   
    BarReader br= new BarReader(f);
    LandscapeBuilder lb= br.getLandscapeBuilder();
   
    new LandscapeTransformer(lb).unlog();
   
    new BarExporter(lb, br.header()).writeToFile(new File(d+"/unlog_"+f.getName()));
   
   
   
}   
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public void writeToFile(File of)throws Exception{
    LandscapeScoringStrand ls= new LandscapeScoringStrand(
            new BarReader(ff).getLandscapeBuilder(),
            new BarReader(fr).getLandscapeBuilder(),
            new BedReader(anno).getGenomicRegionsBuilder()
            );
    ls.writeToBedFile(of);
}
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public void writeToFile(File of)throws Exception{
    LandscapeScoringStrand ls= new LandscapeScoringStrand(
            new BarReader(fr).getLandscapeBuilder(),
            new BarReader(ff).getLandscapeBuilder(),
            new BedReader(anno).getGenomicRegionsBuilder()
            );
    ls.writeToBedFile(of);
}
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Related Classes of fork.lib.bio.anno.genomic.BarReader

  • data.cerevisiae.at.Score
  • data.cerevisiae.histmod.xue2012.BarToWig
  • data.cerevisiae.histmod.xue2012.Score
  • data.cerevisiae.lee2007.NormToLee
  • data.cerevisiae.lee2007.Process
  • data.cerevisiae.lee2007.Score
  • data.cerevisiae.nihroadmap.Score
  • data.cerevisiae.vanbakel2013.ScoreAntisense
  • data.cerevisiae.vanbakel2013.ScoreSense
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