Package fork.lib.bio.seq

Examples of fork.lib.bio.seq.FastaSequenceExtractor

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        File f= fs[i];
        if(FileName.getExt(f).equals("bed")){
            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
            gb= gm.getThreePrimeEnds(150, 0); /////////// modify this
            FastaSequenceExtractor fe= new FastaSequenceExtractor(fastaf, gb, null);

            File of= new File(od+"/"+tag+"_"+FileName.getBaseName(f)+".fasta");
            fe.writeToFastaFile(of);
        }
    }
   
   
   
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public void writeToFile(File out, String tit) throws Exception{
    out.getParentFile().mkdirs();
    BufferedWriter bw= new BufferedWriter(new FileWriter(out));
    BedGraphExporter.writeTitle(bw, tit);
   
    FastaSequenceExtractor se= new FastaSequenceExtractor(gen, gbout);
    SequenceExtractorEntry en;
    while( (en= se.nextEntry())!=null ){
        GenomicRegion gr= en.getGenomicRegion();
        NucleotideSequence seq= NucleotideSequenceParser.parseSequence(en.getSequence());
        double at= seq.atContent();
        bw.write( gr.toBedFormat()+"\t"+ ((double)Math.round(at*100)/100)+"\n" );
    }
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    }
   
   
protected void init() throws Exception{
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    FastaSequenceExtractor se= new FastaSequenceExtractor(sf, gb);
    SequenceExtractorEntry en;
    while((en=se.nextEntry())!=null){
        GenomicRegion reg= en.getGenomicRegion();
        String seq= en.getSequence();
        String id= reg.getID();
        idseq.put(id , seq);
        tab.appendEmptyRow(id);
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Related Classes of fork.lib.bio.seq.FastaSequenceExtractor

  • data.cerevisiae.at.ATContentBp
  • data.cerevisiae.test.regseq.ToSeq
  • data.cerevisiae.tfpwm.ZhuToGene
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