Beispiel #1
0
  public String translate(Sequence s, GeneticCode gncode) {
    String AA = "";
    Sequence n = new Sequence();
    n.setSequence(s.getSequence().toUpperCase());
    int pos = 0;
    boolean found = false;
    // --Find start codon

    //        while(!found&&pos<n.getLen()-2) {
    //            String start=n.getSequence().substring(pos, pos+3);
    //            if (gncode.getStart_code().get(start)!=null) {
    //                AA+=""+gncode.getStart_code().get(start);
    //                pos+=3;
    //                found=true;
    //            }
    //            pos++;
    //        }
    // --return empty string if not found
    //        if (!found) {
    //            Config.log("No Start");
    //            return AA;
    //        }
    pos = start;
    // --Continue
    n.Remove(0, pos); // remove till start

    String codon = n.Remove(0, 3);
    // Config.log(n.getSequence());
    while (!codon.isEmpty() && n.getLen() > 0) {
      // Config.log(codon+" "+gncode.getCode().get(codon));
      String aa = gncode.getCode().get(codon);
      // Config.log(aa);
      if (aa != null) {
        AA += aa;
      } else {
        if (codon.length() == 3) AA += "-";
      }
      codon = n.Remove(0, 3);
    }
    // --Remove ending "*" if found
    if (AA.endsWith("*")) {
      AA = AA.substring(0, AA.length() - 1);
    }
    return AA;
  }
    /**
     * We read file as fasta but we group sequences by iteration
     *
     * @param filename
     * @return
     */
    @Override
    public boolean loadSequences(String filename) {

      this.name = filename;
      try {
        seq.clear(); // Clear the sequence vector and open the file
        BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
        // VARIABLES
        boolean sequenceMode = false;
        Sequence tmp = new Sequence(); // Temp sequence
        StringBuilder tmpsequence = new StringBuilder(); // Temp sequence string
        String stri = ""; // Temp read line

        // Read the file in a buffer an parse at the same time
        // Process :: We read like a fasta file
        Config.log("Reading fasta:" + filename + ":");
        int count = 0;
        String buffer_iteration = ""; // Counter for iterations;
        Pattern iter = Pattern.compile("iterations = ([0-9]*)");
        while (br.ready()) {
          stri = br.readLine();
          Matcher m = iter.matcher(stri);
          if (m.find()) {
            // --Save current Alignment and add to group
            if (!buffer_iteration.isEmpty()) {
              // --Replace name
              if (getNbSequence() > 0) {
                for (Sequence s : getSequences()) {
                  try {
                    String sname =
                        (s.getName().startsWith("AZ") ? s.getName().substring(2) : s.getName());
                    int original_sequence_id = Integer.valueOf(sname);
                    InfoSequence info = df.getInfoSequence(original_sequence_id);
                    // System.out.println(info);
                    s.setName(info.getName());
                    s.setGi(info.getGi());
                    s.setAccession(info.getAccession());
                    s.setAccession_referee(info.getAccession_referee());
                    s.setAbbreviate(info.getAbbreviate());
                    s.setSequence_type(info.getSequence_type());
                    s.setOriginal_id(original_sequence_id);
                    // System.out.println(s.getAbbreviate());
                  } catch (Exception e) {
                  }
                }
                this.setName("Iterations_" + m.group(1) + "_" + name);
                this.setNote("Created on " + Util.returnCurrentDateAndTime());
                this.saveToDatabase();
                this.setId(0);
                this.getSequences().removeAllElements();
              }
              buffer_iteration = stri;
            }
            if (sequenceMode && (stri.equals("") || stri.startsWith(">"))) {
              tmp.setSequence(tmpsequence.toString());
              tmp.loadInfoFromName();
              // Add sequence if not empty
              if (tmp.getSequence().length() > 0) seq.add(tmp);
              tmp = new Sequence();
              tmpsequence = new StringBuilder();
              sequenceMode = false;
            }
            if (sequenceMode) {
              tmpsequence.append(stri);
              count++;
              if (count % 10000 == 0) Config.log("*");
            }
            if (stri.startsWith(">")) {
              // We have a fasta definition
              tmp.setName(stri.substring(1)); // remove >
              sequenceMode = true;
            }
          } // end while
          // Add last read
          if (sequenceMode) {
            tmp.setSequence(tmpsequence.toString());
            tmp.loadInfoFromName();
            if (tmp.getSequence().length() > 0) seq.add(tmp);
            tmp = new Sequence();
          }
          br.close();
          if (seq.size() == 0) {
            if (isDebug()) Config.log("not fasta...");
            return false;
          }
        }
      } catch (Exception e) {
        e.printStackTrace();
        Config.log("Error with " + filename);
        return false;
      }
      if (isDebug()) Config.log("done");

      return true;
    }
Beispiel #3
0
  public String aa_to_dna(Sequence original_dna, Sequence protein, GeneticCode gncode) {
    LinkedList<String> codons = new LinkedList<String>();
    String AA = "";
    String dna = "";
    Sequence n = new Sequence();
    n.setSequence(original_dna.getSequence().toUpperCase());
    int pos = 0;
    boolean found = false;
    // --Find start codon

    //        while(!found&&pos<n.getLen()-2) {
    //            String start=n.getSequence().substring(pos, pos+3);
    //            if (gncode.getStart_code().get(start)!=null) {
    //                AA+=""+gncode.getStart_code().get(start);
    //                codons.add(start);
    //                pos+=3;
    //                found=true;
    //            }
    //            pos++;
    //        }
    // --return empty string if not found
    //        if (!found) {
    //            Config.log("No Start");
    //            return AA;
    //        }

    pos = start;
    // --MAKE THE ORIGINAL TRANSLATION
    n.Remove(0, pos); // remove till start
    String codon = n.Remove(0, 3);
    // --Debug
    // Config.log(n.getSequence());
    while (!codon.isEmpty() && n.getLen() > 0) {
      // Config.log(codon+" "+gncode.getCode().get(codon));
      String aa = gncode.getCode().get(codon);
      // --Debug
      // Config.log(aa);
      if (aa != null) {
        AA += aa;
        codons.add(codon);
      } else {
        if (codon.length() == 3) AA += "-";
      }
      codon = n.Remove(0, 3);
    }
    // --MAKE THE REAL cDNA
    for (int i = 0; i < protein.getLen(); i++) {
      char c = protein.getSequence().charAt(i);
      // Config.log(c);
      if (c == '-' || c == '.') {
        dna += "---";
      } else {
        // --remove stop codon
        String codon_to_add = codons.poll();
        if (codon_to_add != null) {
          if (gncode.getCode().get(codon_to_add).equals("*")) codon_to_add = "---";
          dna += codon_to_add;
        }
      }
    }
    return dna;
  }