Exemplo n.º 1
0
  private ScanAnalysis.Result checkBootScan(PhyloClusterAnalysis pca, AbstractSequence s)
      throws AnalysisException {
    ScanAnalysis sa = null;
    try {
      sa = (ScanAnalysis) pca.getOwner().getAnalysis(pca.getId() + "-scan");
    } catch (Exception e) {
      /* If not available */
      return null;
    }

    return sa.run(s);
  }
Exemplo n.º 2
0
  /**
   * @param pca phylogenetic analysis to run
   * @param s sequence
   * @param blastResult genus matched
   * @param region region used for this analysis
   */
  private void phyloAnalysis(
      PhyloClusterAnalysis pca, AbstractSequence s, Result blastResult, Region region)
      throws AnalysisException, IOException, ParameterProblemException, FileFormatException {
    PhyloClusterAnalysis.Result r = pca.run(s);
    ScanAnalysis.Result scanResult = checkBootScan(pca, s);

    if (r.haveSupport() && (scanResult == null || scanResult.haveSupport())) {
      conclude(
          r,
          new WString("Supported with phylogenetic analysis and bootstrap {1} (>= {2})")
              .arg(r.getConcludedSupport())
              .arg(pca.getCutoff()),
          "type",
          region);

      subgenogroupPhyloAnalysis(s, blastResult, region, r.getConcludedCluster());
    } else conclude("Could not assign", "Not supported by phylogenetic analysis", "type", region);
  }
Exemplo n.º 3
0
  private boolean subgenogroupPhyloAnalysis(
      AbstractSequence s, Result blastResult, Region region, Cluster typeCluster)
      throws AnalysisException, IOException, ParameterProblemException, FileFormatException {
    PhyloClusterAnalysis a =
        getPhyloAnalysis(blastResult.getConcludedCluster().getId(), typeCluster.getId(), region);

    if (a == null) {
      if (region != null) {
        region = null;
        a =
            getPhyloAnalysis(
                blastResult.getConcludedCluster().getId(), typeCluster.getId(), region);

        if (a == null) return false;
      } else {
        List<Region> regions = Collections.emptyList();

        if (blastResult.getReference() != null)
          /*
           * Perhaps we have an analysis for the region covered by the input sequence ?
           */
          regions = findOverlappingRegions(blastResult);

        boolean result = false;
        for (Region r : regions)
          if (subgenogroupPhyloAnalysis(s, blastResult, r, typeCluster)) result = true;

        return result;
      }
    }

    if (region != null) s = cutRegion(s, blastResult, region);

    PhyloClusterAnalysis.Result r = a.run(s);
    ScanAnalysis.Result scanResult = checkBootScan(a, s);

    String phyloName = "phylogenetic subgenogroup analysis within " + typeCluster.getId();

    /*
     * If we are clustering with the outgroup, then clearly we could not identify a variant.
     *
     * WARNING: the following test is based on a variant cluster to start with the same
     * name as the genotype for which it is a variant!
     * This is to differentiate with the outgroup. It would be better to mark the
     * outgroup with some attribute ?
     */

    if (r == null
        || (scanResult != null && !scanResult.haveSupport())
        || r.getConcludedCluster() == null
        || !r.getConcludedCluster().getId().contains(typeCluster.getId())
        || !r.haveSupport())
      conclude("Could not assign", "Not supported by " + phyloName, "subtype", region);
    else
      conclude(
          r,
          new WString("Supported with " + phyloName + " and bootstrap {1} (&gt;= {2})")
              .arg(r.getConcludedSupport())
              .arg(a.getCutoff()),
          "subtype",
          region);

    return true;
  }