Package fork.lib.base.file.io.txt

Examples of fork.lib.base.file.io.txt.MarkReader

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        this.f=tf;
        init();
    }
   
protected void init() throws Exception{
    mr= new MarkReader(f,"-primary");
    mr.setIfFirstChar(false);
}
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    File d= new File(dir+"/other_datasets/cai_2011_h3k9ac");
    File f= new File(d+"/GSM711896.wig"), out=new File(d+"/h3k9ac_cai2011.wig");
   
   
   
    MarkReader mr= new MarkReader(f, "variableStep");
    MarkEntry en;
    LandscapeBuilder lb= new LandscapeBuilder();
    while((en=mr.nextEntry())!=null){
        String chr= en.tit.split("chrom=")[1].split("\t")[0];
       
        if(!chr.equals("chrM")){
            ArrayList<String> rs= en.chunk;
            int ps= 1;
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    }
   
   
   
protected void init() throws Exception{
    MarkReader mr= new MarkReader(file,">");
    MarkEntry en;
    while((en=mr.nextEntry())!=null){
        sets.add( new GeneSet(en.getChunk(), en.getTitle()) );
    }
    mr.close();
}
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    File f= new File(dir+"/data/tf/badis_2008_tf.txt");
    File od= new File(dir+"/data/tf/"+FileName.getBaseName(f));
   
   
    MarkReader ff= new MarkReader(f,">");
    MarkEntry en;
   
    while( (en=ff.nextEntry())!=null ){
        String nm= en.getTitle().split("_TRH1")[0];
        NamedTable<Character,Integer,Double> tab= new NamedTable<>();
        ArrayList<String> ch= en.getChunk();
        for(int i=1; i<ch.size() ; i++){
            String[] ss= ch.get(i).split("\t");
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  • data.cerevisiae.histmod.cai2011.ToWig
  • data.cerevisiae.tfpwm.BadisToLandscape
  • data.cerevisiae.tfpwm.ZhuToLandscape
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