BioJava: How to get All frame 1 to 6 of DNA to Protein translation for All Genetic Code?

Question

[rushikesh4381]

How to get All frame 1 to 6 of DNA to Protein translation for all Genetic Code using biojava.

[Pierre Lindenbaum]

sounds like homework . what have you tried ?

[GouthamAtla]

Looks like you have not tried to write a program and also you have not even tried to search in google as well.

[rushikesh4381]

Below class only translates for Universal genetic code but not for all genetic code ..... I am trying for all conversion for all genetic code

public class Check_Transaltion {

    public static void main(String[] args) {

        String filename = "";
        String type = "";

        try {
            if (args.length != 0) {
                filename = args[0];
                type = args[1].toUpperCase();
            }else{
        //        filename =System.getProperty("java.io.tmpdir")+"/MYOZ1.fasta";
                type="DNA";
                FileOutputStream f = new FileOutputStream(new File("/home/arraygen/Desktop/MYOZ1.fasta"));
                PrintStream ps = new PrintStream(f);
                ps.print(MYOZ1);
                ps.close();
                f.close();
            }

            SymbolTokenization toke = AlphabetManager.alphabetForName(type)
                    .getTokenization("token");

            BufferedReader br = new BufferedReader(new FileReader("/home/arraygen/Desktop/MYOZ1.fasta"));

            SequenceIterator seqi = RichSequence.IOTools.readFasta(br,
                    toke, null);

            // for each sequence
            while (seqi.hasNext()) {
                Sequence seq = seqi.nextSequence();

                // for each frame
                for (int I = 0; I < 3; i++) {
                    SymbolList prot;
                    Sequence trans;

                    // take the reading frame
                    // remember that in a SymbolList the first element has
                    // index= 1
                    // remember that if the length of the list evenly divisible
                    // by three an IllegalArgumentException will be thrown
                    SymbolList syms = seq.subList(i + 1, seq.length()
                            - (seq.length() - i) % 3);

                    // if it is DNA transcribe it to RNA
                    if (syms.getAlphabet() == DNATools.getDNA()) {
                        syms = DNATools.toRNA(syms);
                    }

                    // output forward translation to STDOUT
                    prot = RNATools.translate(syms);
                    trans = SequenceTools.createSequence(prot, "", seq
                            .getName()
                            + "TranslationFrame: +" + i,
                            Annotation.EMPTY_ANNOTATION);

                    /*
                     * This method is deprecated since BioJava 1.5
                     * SeqIOTools.writeFasta(System.out, trans);
                     */
                    RichSequence.IOTools.writeFasta(System.out, trans, null);

                    // output reverse frame translation to STDOUT
                    syms = RNATools.reverseComplement(syms);
                    prot = RNATools.translate(syms);
                    trans = SequenceTools.createSequence(prot, "", seq
                            .getName()
                            + " TranslationFrame: -" + i,
                            Annotation.EMPTY_ANNOTATION);
                    /*
                     * This method is deprecated since BioJava 1.5
                     * SeqIOTools.writeFasta(System.out, trans);
                     */

        //            System.out.println(trans.seqString());
    //                trans.seqString()

                    RichSequence.IOTools.writeFasta(System.out, trans, null);
                }
            }
            br.close();
        } catch (IOException e) {
            e.printStackTrace();
        } catch (IllegalAlphabetException e) {
            e.printStackTrace();
        } catch (NoSuchElementException e) {
            e.printStackTrace();
        } catch (BioException e) {
            e.printStackTrace();
        }
    }

    private static String MYOZ1 = ">gi|21359948|ref|NM_021245.2| Homo sapiens myozenin 1 (MYOZ1), mRNA "
            + "\n"
            + "GTTTCTCCCTAAGTGCTTCTTTGGATCTCAGGCTCTAGGTGCAATGTGAAGGGGAGTCCCTGGGCAGACTGATCCCTGGC"
            + "TCAGACAGTTCAGTGGGAGAATCCCAAAGGCCTTTTCCCTCCTTCCTGAGCCTCCGGGCAAGGAGGGAGGGATCTTGGTT"
            + "CCAGGGTCTCAGTACCCCCTGTGCCATTTGAGCTGCTTGCGCTCATCATCTCTATTAATAACCAACTTCCCTCCCCCACT"
            + "GCCAGTGCTGCCCCCACGCCTGCCCAGCTCGTGTTCTCCGGTCACAGCAGCTCAGTCCTCCAAAGCTGCTGGACCCCAGG"
            + "GAGAGCTGACCACTGCCCGAGCAGCCGGCTGAATCCACCTCCACAATGCCGCTCTCAGGAACCCCGGCCCCTAATAAGAA"
            + "GAGGAAATCCAGCAAGCTGATCATGGAACTCACTGGAGGTGGACAGGAGAGCTCAGGCTTGAACCTGGGCAAAAAGATCA"
            + "GTGTCCCAAGGGATGTGATGTTGGAGGAACTGTCGCTGCTTACCAACCGGGGCTCCAAGATGTTCAAACTGCGGCAGATG"
            + "AGGGTGGAGAAGTTTATTTATGAGAACCACCCTGATGTTTTCTCTGACAGCTCAATGGATCACTTCCAGAAGTTCCTTCC"
            + "AACAGTGGGGGGACAGCTGGGCACAGCTGGTCAGGGATTCTCATACAGCAAGAGCAACGGCAGAGGCGGCAGCCAGGCAG"
            + "GGGGCAGTGGCTCTGCCGGACAGTATGGCTCTGATCAGCAGCACCATCTGGGCTCTGGGTCTGGAGCTGGGGGTACAGGT"
            + "GGTCCCGCGGGCCAGGCTGGCAGAGGAGGAGCTGCTGGCACAGCAGGGGTTGGTGAGACAGGATCAGGAGACCAGGCAGG"
            + "CGGAGAAGGAAAACATATCACTGTGTTCAAGACCTATATTTCCCCATGGGAGCGAGCCATGGGGGTTGACCCCCAGCAAA"
            + "TGAACCCCTGGTCCTCTACAACCAAAACCTCTCCAACAGGCCTTCTTTCAATCGAACCCCTATTCCCTGGCTGAGCTCTG"
            + "GGGAGCCTGTAGACTACAACGTGGATATTGGCATCCCCTTGGATGGAGAAACAGAGGAGCTGTGAGGTGTTTCCTCCTCT"
            + "GATTTGCATCATTTCCCCTCTCTGGCTCCAATTTGGAGAGGGAATGCTGAGCAGATAGCCCCCATTGTTAATCCAGTATC"
            + "CTTATGGGAATGGAGGGAAAAAGGAGAGATCTACCTTTCCATCCTTTACTCCAAGTCCCCACTCCACGCATCCTTCCTCA"
            + "CCAACTCAGAGCTCCCCTTCTACTTGCTCCATATGGAACCTGCTCGTTTATGGAATTTGCTCTGCCACCAGTAACAGTCA"
            + "ATAAACTTCAAGGAAAATGAAAAAAAA";

}