Package fork.lib.bio.seq

Examples of fork.lib.bio.seq.FastaReader.nextEntry()

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    FrequencyCount<String> fcg= new FrequencyCount();
    FastaReader frg= new FastaReader(genomef);
    FastaEntry eng;
    while( (eng=frg.nextEntry())!=null ){
        String s= eng.getSequence();
        for( int i=0; i<s.length()-size; i++ ){
            String ss= s.substring(i, i+size);
            fcg.add(ss);
        }
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            FastaReader fr= new FastaReader(f);
            FastaEntry en;
            FrequencyCount<String> fc= new FrequencyCount<>();


            while( (en=fr.nextEntry())!=null ){
                String s= en.getSequence();
                for( int i=0; i<s.length()-size; i++ ){
                    String ss= s.substring(i, i+size);
                    fc.add(ss);
                }
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    File gen= new File(dir+"/anno/genomes/sacCer1/sacCer1.fa");
    FastaReader fr= new FastaReader(gen);
    BufferedWriter bw= new BufferedWriter(new FileWriter(new File(dir+"/anno/sacCer1_chr.bed")));
    FastaEntry en;
    while( (en=fr.nextEntry())!=null ){
        String chr= en.getTitle();
        int l= en.getSequence().length();
        bw.write(chr+"\t0\t"+l+"\t"+chr+"\t0\t+\n");
    }
    bw.close();
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