Package fork.lib.bio.seq

Examples of fork.lib.bio.seq.GetSequenceFasta

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    File[] fs= dir.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        String fn= FileName.getBaseName(f);
        if(fn.indexOf("chr")==0){
            chrGet.put(fn, new GetSequenceFasta(f));;
        }
    }
    idReg= new BedReader(bedf).getIDToRegionMap();
}
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        String id = ids.get(i);
        DirectionalGenomicRegion gr= (DirectionalGenomicRegion) idReg.get(id);
        if(gr==null){
            continue;
        }
        GetSequenceFasta gs= chrGet.get(gr.chr);
        if(gs!=null){
            String seq= gs.getSequence(gr);
            if(gr.isOnReverseStrand()){
                seq= NucleotideSequenceParser.parseSequence(seq).complementary().toString();
            }
            for( int j=0; j<seq.length(); j++ ){
                fc.add(seq.charAt(j));
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public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
    File d = new File(dir+"/other_datasets/lee_2007_nucleosome/pref");
    File od= new File(d+"/seq");
   
    GetSequenceFasta get= new GetSequenceFasta(new File(dir+"/anno/genomes/sacCer1/sacCer1.fa"));
   
    for( int i=0; i<10; i++ ){
        File f= new File(d+"/bin_"+i+".bed");
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
        ToSeq tt= new ToSeq(gb, get);
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Related Classes of fork.lib.bio.seq.GetSequenceFasta

  • data.cerevisiae.lee2007.pref.ToSeq
  • data.cerevisiae.test.compseq.SeqComposition
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