Ejemplo n.º 1
0
  public String toString(boolean useSeqOntology, boolean useHgvs) {
    // Get data to show
    String geneId = "", geneName = "", bioType = "", transcriptId = "", exonId = "", customId = "";
    int exonRank = -1;

    if (marker != null) {
      // Gene Id, name and biotype
      Gene gene = getGene();
      Transcript tr = getTranscript();

      // CDS size info
      if (gene != null) {
        geneId = gene.getId();
        geneName = gene.getGeneName();
        bioType = getBiotype();
      }

      // Update trId
      if (tr != null) transcriptId = tr.getId();

      // Exon rank information
      Exon exon = getExon();
      if (exon != null) {
        exonId = exon.getId();
        exonRank = exon.getRank();
      }

      // Regulation
      if (isRegulation()) bioType = ((Regulation) marker).getCellType();
    }

    // Add seqChage's ID
    if (!variant.getId().isEmpty()) customId += variant.getId();

    // Add custom markers
    if ((marker != null) && (marker instanceof Custom))
      customId += (customId.isEmpty() ? "" : ";") + marker.getId();

    // CDS length
    int cdsSize = getCdsLength();

    String errWarn = error + (error.isEmpty() ? "" : "|") + warning;

    String aaChange = "";
    if (useHgvs) aaChange = getHgvs();
    else aaChange = ((aaRef.length() + aaAlt.length()) > 0 ? aaRef + "/" + aaAlt : "");

    return errWarn //
        + "\t"
        + geneId //
        + "\t"
        + geneName //
        + "\t"
        + bioType //
        + "\t"
        + transcriptId //
        + "\t"
        + exonId //
        + "\t"
        + (exonRank >= 0 ? exonRank : "") //
        + "\t"
        + effect(false, false, false, useSeqOntology) //
        + "\t"
        + aaChange //
        + "\t"
        + ((codonsRef.length() + codonsAlt.length()) > 0 ? codonsRef + "/" + codonsAlt : "") //
        + "\t"
        + (codonNum >= 0 ? (codonNum + 1) : "") //
        + "\t"
        + (codonDegeneracy >= 0 ? codonDegeneracy + "" : "") //
        + "\t"
        + (cdsSize >= 0 ? cdsSize : "") //
        + "\t"
        + (codonsAroundOld.length() > 0 ? codonsAroundOld + " / " + codonsAroundNew : "") //
        + "\t"
        + (aasAroundOld.length() > 0 ? aasAroundOld + " / " + aasAroundNew : "") //
        + "\t"
        + customId //
    ;
  }
Ejemplo n.º 2
0
  /**
   * Name of the regions hit by a marker
   *
   * @param marker
   * @param showGeneDetails
   * @param compareTemplate
   * @param id : Only use genes or transcripts matching this ID
   * @return
   */
  public Set<String> regions(
      Marker marker, boolean showGeneDetails, boolean compareTemplate, String id) {
    if (Config.get().isErrorOnMissingChromo() && isChromosomeMissing(marker))
      throw new RuntimeEOFException("Chromosome missing for marker: " + marker);

    boolean hitChromo = false;
    HashSet<String> hits = new HashSet<String>();

    Markers intersects = query(marker);
    if (intersects.size() > 0) {
      for (Marker markerInt : intersects) {

        if (markerInt instanceof Chromosome) {
          hitChromo = true; // OK (we have to hit a chromosome, otherwise it's an error
          hits.add(markerInt.getClass().getSimpleName()); // Add marker name to the list
        } else if (markerInt instanceof Gene) {
          // Analyze Genes
          Gene gene = (Gene) markerInt;
          regionsAddHit(hits, gene, marker, showGeneDetails, compareTemplate);

          // For all transcripts...
          for (Transcript tr : gene) {
            if ((id == null)
                || gene.getId().equals(id)
                || tr.getId().equals(id)) { // Mathes ID? (...or no ID to match)

              // Does it intersect this transcript?
              if (tr.intersects(marker)) {
                regionsAddHit(hits, tr, marker, showGeneDetails, compareTemplate);

                // Does it intersect a UTR?
                for (Utr utr : tr.getUtrs())
                  if (utr.intersects(marker))
                    regionsAddHit(hits, utr, marker, showGeneDetails, compareTemplate);

                // Does it intersect an exon?
                for (Exon ex : tr)
                  if (ex.intersects(marker))
                    regionsAddHit(hits, ex, marker, showGeneDetails, compareTemplate);

                // Does it intersect an intron?
                for (Intron intron : tr.introns())
                  if (intron.intersects(marker))
                    regionsAddHit(hits, intron, marker, showGeneDetails, compareTemplate);
              }
            }
          }
        } else {
          // No ID to match?
          if (id == null) regionsAddHit(hits, markerInt, marker, showGeneDetails, compareTemplate);
          else {
            // Is ID from transcript?
            Transcript tr = (Transcript) markerInt.findParent(Transcript.class);
            if ((tr != null) && (tr.getId().equals(id))) {
              regionsAddHit(
                  hits,
                  markerInt,
                  marker,
                  showGeneDetails,
                  compareTemplate); // Transcript ID matches => count
            } else {
              // Is ID from gene?
              Gene gene = (Gene) markerInt.findParent(Gene.class);
              if ((gene != null) && (gene.getId().equals(id)))
                regionsAddHit(
                    hits,
                    markerInt,
                    marker,
                    showGeneDetails,
                    compareTemplate); // Gene ID matches => count
            }
          }
        }
      }
    }

    if (!hitChromo) throw new RuntimeException("ERROR: Out of chromosome range. " + marker);
    return hits;
  }