Exemplo n.º 1
0
 /* (non-Javadoc)
  * @see edu.mit.csail.cgs.utils.Factory#createObject()
  */
 public ChipChipMLE createObject() {
   try {
     return ds.getMLE(name, version);
   } catch (NotFoundException nfe) {
     throw new IllegalArgumentException(super.toString());
   }
 }
Exemplo n.º 2
0
  public static void main(String args[]) throws Exception {
    Genome genome = Args.parseGenome(args).cdr();
    ChipChipDataset dataset = new ChipChipDataset(genome);
    List<Region> regions = Args.parseRegionsOrDefault(args);

    double means[] = new double[CGHCallExpander.numStates],
        stddevs[] = new double[CGHCallExpander.numStates];
    String[] pieces =
        Args.parseString(
                args,
                "low",
                String.format(
                    "%f;%f",
                    CGHCallExpander.defaultParams[0][0],
                    Math.sqrt(CGHCallExpander.defaultParams[0][1])))
            .split(";");
    means[CGHCallExpander.LOW] = Double.parseDouble(pieces[0]);
    stddevs[CGHCallExpander.LOW] = Math.pow(Double.parseDouble(pieces[1]), 2);

    pieces =
        Args.parseString(
                args,
                "middle",
                String.format(
                    "%f;%f",
                    CGHCallExpander.defaultParams[0][0],
                    Math.sqrt(CGHCallExpander.defaultParams[0][1])))
            .split(";");
    means[CGHCallExpander.ONE] = Double.parseDouble(pieces[0]);
    stddevs[CGHCallExpander.ONE] = Math.pow(Double.parseDouble(pieces[1]), 2);

    pieces =
        Args.parseString(
                args,
                "high",
                String.format(
                    "%f;%f",
                    CGHCallExpander.defaultParams[0][0],
                    Math.sqrt(CGHCallExpander.defaultParams[0][1])))
            .split(";");
    means[CGHCallExpander.HIGH] = Double.parseDouble(pieces[0]);
    stddevs[CGHCallExpander.HIGH] = Math.pow(Double.parseDouble(pieces[1]), 2);

    for (ExptNameVersion env : Args.parseENV(args)) {
      ChipChipData ccd = dataset.getData(env);
      CGHCallExpander cgh = new CGHCallExpander(ccd);
      cgh.setStateParameters(
          CGHCallExpander.LOW, means[CGHCallExpander.LOW], stddevs[CGHCallExpander.LOW]);
      cgh.setStateParameters(
          CGHCallExpander.ONE, means[CGHCallExpander.ONE], stddevs[CGHCallExpander.ONE]);
      cgh.setStateParameters(
          CGHCallExpander.HIGH, means[CGHCallExpander.HIGH], stddevs[CGHCallExpander.HIGH]);
      cgh.resetHMM();
      for (Region r : regions) {
        List<ScoredRegion> calls = cgh.executeList(r);
        for (ScoredRegion call : calls) {
          System.out.println(call.getScore() + "\t" + call.regionString());
        }
      }
    }
  }