Example #1
0
  @Override
  protected void execute() {
    try {

      // update status
      jobStatus.addStatusMessage("10", "Preparing data");

      // infrared connector
      //			DBConnector dbConnector = new DBConnector(species, new File(babelomicsHomePath +
      // "/conf/infrared.properties"));

      // prepare params
      prepare();

      // run fatigo's
      if (filterList.size() == 0 && !isYourAnnotations) {
        throw new ParseException("No biological database selected (eg. --go-bp)");
      } else {

        // save id lists
        IOUtils.write(outdir + "/ranked_list.txt", rankedList.toString());
        result.addOutputItem(
            new Item(
                "ranked_list",
                "ranked_list.txt",
                "Ranked list",
                Item.TYPE.FILE,
                Arrays.asList("RANKED_LIST", "CLEAN"),
                new HashMap<String, String>(),
                "Input data"));

        // order ranked list and save genes and rank separately
        //				FatiScan fatiscan = new
        // FatiScan(rankedList,null,dbConnector,FatiScan.DEFAULT_NUMBER_OF_PARTITIONS,testMode,outputFormat,order,duplicatesMode);
        FatiScan fatiscan =
            new FatiScan(
                rankedList,
                null,
                null,
                FatiScan.DEFAULT_NUMBER_OF_PARTITIONS,
                testMode,
                outputFormat,
                order,
                duplicatesMode);
        fatiscan.prepareLists();
        IOUtils.write(outdir + "/id_list.txt", fatiscan.getIdList());
        result.addOutputItem(
            new Item(
                "id_list",
                "id_list.txt",
                "Id list (sorted)",
                Item.TYPE.FILE,
                Arrays.asList("IDLIST", "SORTED"),
                new HashMap<String, String>(),
                "Input data"));
        IOUtils.write(outdir + "/statistic.txt", ListUtils.toStringArray(fatiscan.getStatistic()));
        result.addOutputItem(
            new Item(
                "statistic",
                "statistic.txt",
                "Statistic (sorted)",
                Item.TYPE.FILE,
                Arrays.asList("STATISTIC", "SORTED"),
                new HashMap<String, String>(),
                "Input data"));

        // significant count
        significantCount = new ArrayList<StringBuilder>();
        for (int i = 0; i < DEFAULT_PVALUES.length; i++) {
          significantCount.add(new StringBuilder("#DB\tNÂș of significant terms\n"));
        }

        // annotation report
        annotationReport = new StringBuilder();
        annotationReport.append("#DB").append("\t").append("Number of annotations").append("\n");

        // do fatiscans
        double progress = 20;
        double inc = 60.0 / filterList.size();
        for (FunctionalFilter filter : filterList) {
          doTest(rankedList, filter, method);
          jobStatus.addStatusMessage("" + progress, "Executing test");
          progress += inc;
        }

        // update status
        jobStatus.addStatusMessage("90", "Executing test");

        if (isYourAnnotations) {
          doYourAnnotationsTest(rankedList, yourAnnotations, method);
        }

        // update status
        jobStatus.addStatusMessage("95", "Saving results");

        saveAnnotationsReport();

        // save significant count table
        for (int i = 0; i < DEFAULT_PVALUES.length; i++) {
          IOUtils.write(
              outdir + "/significant_count_" + pvalueFormatter.format(DEFAULT_PVALUES[i]) + ".txt",
              significantCount.get(i).toString());
        }
        result
            .getOutputItems()
            .add(
                3,
                new Item(
                    "significant",
                    "significant_count_${pvalue}.txt",
                    "Number of significant terms per DB",
                    Item.TYPE.FILE,
                    Arrays.asList("TABLE,SUMMARY_TABLE,SIGNIFICANT_COUNT_TABLE"),
                    new HashMap<String, String>(),
                    "Significant Results"));
        result.addMetaItem(new Item("flags", "SHOW_PVALUES", "", TYPE.MESSAGE));
      }

    } catch (Exception e) {
      e.printStackTrace();
    }
  }
Example #2
0
  public void executeAnova() {

    DoubleMatrix matrix = null;
    List<String> vars = new ArrayList<String>();
    List<Integer> indices = new ArrayList<Integer>();
    List<String> values = dataset.getVariables().getByName(className).getValues();

    if (values.size() == classValues.size()) {
      matrix = dataset.getDoubleMatrix();
      vars = values;
    } else {
      for (int i = 0; i < values.size(); i++) {
        if (classValues.contains(values.get(i))) {
          indices.add(i);
          vars.add(values.get(i));
        }
      }
      matrix = dataset.getSubMatrixByColumns(ListUtils.toIntArray(indices));
    }

    try {
      Dataset subDataset = dataset.getSubDataset(className, classValues);

      // apply test and multiple test correction according
      //
      AnovaTest anova = new AnovaTest(matrix, vars);
      TestResultList<AnovaTestResult> res = anova.compute();
      DiffExpressionUtils.multipleTestCorrection(res, correction);

      // create output file
      //
      int[] columnOrder =
          ListUtils.order(subDataset.getVariables().getByName(className).getValues());
      int[] rowOrder = ListUtils.order(ArrayUtils.toList(res.getStatistics()), true);

      DataFrame dataFrame = new DataFrame(subDataset.getFeatureNames().size(), 0);
      dataFrame.addColumn(
          "statistic",
          ListUtils.toStringList(
              ListUtils.ordered(ArrayUtils.toList(res.getStatistics()), rowOrder)));
      dataFrame.addColumn(
          "p-value",
          ListUtils.toStringList(ListUtils.ordered(ArrayUtils.toList(res.getPValues()), rowOrder)));
      dataFrame.addColumn(
          "adj. p-value",
          ListUtils.toStringList(
              ListUtils.ordered(ArrayUtils.toList(res.getAdjPValues()), rowOrder)));
      dataFrame.setRowNames(ListUtils.ordered(subDataset.getFeatureNames(), rowOrder));

      FeatureData featureData = new FeatureData(dataFrame);
      File file = new File(outdir + "/" + test + ".txt");
      featureData.save(file);
      if (file.exists()) {
        result.addOutputItem(
            new Item(
                test + "file",
                file.getName(),
                "Anova output file",
                TYPE.FILE,
                new ArrayList<String>(2),
                new HashMap<String, String>(2),
                "Anova output files"));
      }

      // getting significative genes
      //
      DiffExpressionUtils.addSignificativeResults(
          subDataset,
          test,
          "statistic",
          res.getStatistics(),
          "adj. p-value",
          res.getAdjPValues(),
          "p-value",
          res.getPValues(),
          null,
          null,
          null,
          null,
          className,
          columnOrder,
          pValue,
          maxDisplay,
          this);
      DiffExpressionUtils.createFatiScanRedirection(dataFrame, test, "statistic", result, outdir);
    } catch (Exception e) {
      e.printStackTrace();
      abort(
          "exception_executeanova_classcomparison",
          "error running anova",
          "error running anova: " + e.getMessage(),
          "error running anova: " + e.getMessage());
    }
  }
Example #3
0
  /**
   * @throws InvalidColumnIndexException
   * @throws IOException
   */
  public void executeLimma() {

    Limma limma = null;
    if (classValues.size() > 2) {
      limma = new Limma(babelomicsHomePath + "/bin/diffexp/limma_multiclasses.r");
    } else if (classValues.size() == 2) {
      limma = new Limma(babelomicsHomePath + "/bin/diffexp/limma_twoclasses.r");
    } else if (classValues.size() == 1) {
      limma = new Limma(babelomicsHomePath + "/bin/diffexp/limma_oneclass.r");
    } else {
      abort(
          "testmismatched_executelimma_classcomparison",
          "test " + test + " not supported for " + classValues.size() + "-class test",
          "test " + test + " not supported for " + classValues.size() + "-class test",
          "test " + test + " not supported for " + classValues.size() + "-class test");
    }

    // System.out.println("dataset = " + dataset.toString());
    System.out.println("class name = " + className);

    limma.setInputFilename(dataset.getDatasetFile().getAbsolutePath());
    limma.setClasses(dataset.getVariables().getByName(className).getValues());
    limma.setContrast(classValues);

    try {
      Dataset subDataset = dataset.getSubDataset(className, classValues);

      // apply test and multiple test correction according
      //
      TestResultList<LimmaTestResult> res = limma.compute();
      DiffExpressionUtils.multipleTestCorrection(res, correction);

      // create output file
      //
      int[] columnOrder =
          ListUtils.order(subDataset.getVariables().getByName(className).getValues());
      int[] rowOrder = ListUtils.order(ArrayUtils.toList(res.getStatistics()), true);

      DataFrame dataFrame = new DataFrame(subDataset.getFeatureNames().size(), 0);
      dataFrame.addColumn(
          "statistic",
          ListUtils.toStringList(
              ListUtils.ordered(ArrayUtils.toList(res.getStatistics()), rowOrder)));
      dataFrame.addColumn(
          "p-value",
          ListUtils.toStringList(ListUtils.ordered(ArrayUtils.toList(res.getPValues()), rowOrder)));
      dataFrame.addColumn(
          "adj. p-value",
          ListUtils.toStringList(
              ListUtils.ordered(ArrayUtils.toList(res.getAdjPValues()), rowOrder)));
      dataFrame.setRowNames(ListUtils.ordered(subDataset.getFeatureNames(), rowOrder));

      FeatureData featureData = new FeatureData(dataFrame);
      File file = new File(outdir + "/" + test + ".txt");
      featureData.save(file);
      if (file.exists()) {
        result.addOutputItem(
            new Item(
                test + "file",
                file.getName(),
                "Limma output file",
                TYPE.FILE,
                new ArrayList<String>(2),
                new HashMap<String, String>(2),
                "Limma output files"));
      }

      // getting significative genes
      //
      DiffExpressionUtils.addSignificativeResults(
          subDataset,
          test,
          "statistic",
          res.getStatistics(),
          "adj. p-value",
          res.getAdjPValues(),
          "p-value",
          res.getPValues(),
          null,
          null,
          null,
          null,
          className,
          columnOrder,
          pValue,
          maxDisplay,
          this);
      DiffExpressionUtils.createFatiScanRedirection(dataFrame, test, "statistic", result, outdir);
    } catch (Exception e) {
      e.printStackTrace();
      abort(
          "exception_executelimma_classcomparison",
          "error running limma",
          "error running limma: " + e.toString(),
          "error running limma: " + e.toString());
    }
  }
Example #4
0
  public void executeT() {

    int[] cols = dataset.getColumnIndexesByVariableValue(className, classValues.get(0));
    DoubleMatrix sample1 = dataset.getSubMatrixByColumns(cols);

    cols = dataset.getColumnIndexesByVariableValue(className, classValues.get(1));
    DoubleMatrix sample2 = dataset.getSubMatrixByColumns(cols);

    try {
      Dataset subDataset = dataset.getSubDataset(className, classValues);

      // apply test and multiple test correction according
      //
      TTest tTest = new TTest();
      TestResultList<TTestResult> res = tTest.tTest(sample1, sample2);
      DiffExpressionUtils.multipleTestCorrection(res, correction);

      // create output file
      //
      int[] columnOrder =
          ListUtils.order(subDataset.getVariables().getByName(className).getValues());
      int[] rowOrder = ListUtils.order(ArrayUtils.toList(res.getStatistics()), true);

      DataFrame dataFrame = new DataFrame(subDataset.getFeatureNames().size(), 0);
      dataFrame.addColumn(
          "statistic",
          ListUtils.toStringList(
              ListUtils.ordered(ArrayUtils.toList(res.getStatistics()), rowOrder)));
      dataFrame.addColumn(
          "p-value",
          ListUtils.toStringList(ListUtils.ordered(ArrayUtils.toList(res.getPValues()), rowOrder)));
      dataFrame.addColumn(
          "adj. p-value",
          ListUtils.toStringList(
              ListUtils.ordered(ArrayUtils.toList(res.getAdjPValues()), rowOrder)));
      dataFrame.setRowNames(ListUtils.ordered(subDataset.getFeatureNames(), rowOrder));

      FeatureData featureData = new FeatureData(dataFrame);
      File file = new File(outdir + "/t.txt");
      featureData.save(file);
      if (file.exists()) {
        result.addOutputItem(
            new Item(
                "tfile",
                file.getName(),
                "T-test output file",
                TYPE.FILE,
                new ArrayList<String>(),
                new HashMap<String, String>(),
                "T-test output files"));
      }

      // getting significative genes
      //
      DiffExpressionUtils.addSignificativeResults(
          subDataset,
          test,
          "statistic",
          res.getStatistics(),
          "adj. p-value",
          res.getAdjPValues(),
          "p-value",
          res.getPValues(),
          null,
          null,
          null,
          null,
          className,
          columnOrder,
          pValue,
          maxDisplay,
          this);
      DiffExpressionUtils.createFatiScanRedirection(dataFrame, test, "statistic", result, outdir);
    } catch (Exception e) {
      e.printStackTrace();
      abort("exception_executet_classcomparison", "ERROR", "Error running t-test", "");
    }
  }