public static void main(String[] args) {
    File column = new File(args[0]);
    try {
      // how many different dbs are present
      LinkedHashMap dbs = new LinkedHashMap();
      BufferedReader in = new BufferedReader(new FileReader(column));
      String line;
      int index = 0;
      while ((line = in.readLine()) != null) {
        if (line.trim().length() == 0) continue;
        String[] tokens = line.split("\\|");
        for (int i = 0; i < tokens.length; i += 2) {
          if (dbs.containsKey(tokens[i]) == false) {
            dbs.put(tokens[i], new Integer(index++));
          }
        }
      }
      in.close();
      // print header
      Iterator it = dbs.keySet().iterator();
      while (it.hasNext()) {
        String c = (String) it.next();
        System.out.print("Reporter BioSequence DatabaseEntry [" + c + "]\t");
      }
      System.out.println();
      // print lines
      in = new BufferedReader(new FileReader(column));
      int numColumns = dbs.size();
      while ((line = in.readLine()) != null) {
        if (line.trim().length() == 0) {
          System.out.println();
        } else {
          String[] columns = new String[numColumns];
          String[] tokens = line.split("\\|");
          for (int i = 0; i < tokens.length; i += 2) {
            // System.out.println(line+"Tok"+tokens[i]);
            int columnIndex = ((Integer) dbs.get(tokens[i])).intValue();
            if (columns[columnIndex] == null) columns[columnIndex] = tokens[i + 1];
            else columns[columnIndex] = columns[columnIndex] + ";" + tokens[i + 1];
          }
          // print it
          for (int i = 0; i < numColumns; i++) {
            if (columns[i] == null) columns[i] = "";
          }
          System.out.println(Misc.stringArrayToString(columns, "\t"));
        }
      }
      in.close();

    } catch (Exception e) {
      e.printStackTrace();
    }
  }
示例#2
0
  /**
   * Makes a stair step heat map from an array of windows in bar format. One per chromosome. Don't
   * forget to set the barDirectory and score Index!!!!!!!
   */
  public void makeStairStepBarFiles() {
    // make bar parser
    BarParser bp = new BarParser();
    bp.setZipCompress(true);
    HashMap<String, String> tagVals = new HashMap<String, String>();
    tagVals.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_STAIRSTEP);
    tagVals.put(BarParser.GRAPH_TYPE_COLOR_TAG, "#FF00FF"); // fusha
    tagVals.put(BarParser.SOURCE_TAG, bedFile.toString());

    // for each chromosome
    System.out.print("Printing... ");
    Iterator<String> it = bedLinesHash.keySet().iterator();
    while (it.hasNext()) {
      chromosome = it.next();
      System.out.print(chromosome + " ");
      windows = bedLinesHash.get(chromosome);
      // add blocks
      assembleBlocks();
      // balance by adding max or min at zero base
      balanceValues();
      // write bar file
      File barFile = new File(barDirectory, chromosome + ".bar");
      bp.writeBarFile(
          barFile,
          chromosome,
          genomeVersion,
          '.',
          Num.arrayListOfIntegerToInts(bases),
          Num.arrayListOfFloatToArray(values),
          tagVals);
      // clear ArrayLists
      bases.clear();
      values.clear();
    }
    System.out.println();
  }