Example #1
0
  /**
   * Load GWAS PLINK result file
   *
   * @param locator
   * @param newTracks
   * @throws IOException
   */
  private void loadGWASFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
      throws IOException {

    GWASParser gwasParser = new GWASParser(locator, genome);
    GWASData gwasData = gwasParser.parse();

    GWASTrack gwasTrack =
        new GWASTrack(locator, locator.getPath(), locator.getFileName(), gwasData, gwasParser);
    newTracks.add(gwasTrack);
  }
Example #2
0
  public static Sorter getSorter(File inputFile, File outputFile) {

    String shortFN = inputFile.getName().toLowerCase();
    if (shortFN.endsWith(".txt")) {
      shortFN = shortFN.substring(0, shortFN.length() - 4);
    }
    if (shortFN.endsWith(".cn")
        || shortFN.endsWith(".xcn")
        || shortFN.endsWith(".snp")
        || shortFN.endsWith(".igv")) {
      return new CNSorter(inputFile, outputFile);
    } else if (shortFN.endsWith(".sam")) {
      return new SAMSorter(inputFile, outputFile);
    } else if (shortFN.endsWith(".aligned")
        || shortFN.endsWith(".bed")
        || shortFN.endsWith(".bedgraph")
        || shortFN.endsWith(".bdg")) {
      return new BedSorter(inputFile, outputFile);
    } else if (GFFFeatureSource.isGFF(shortFN)) {
      return new GFFSorter(inputFile, outputFile);
    } else if (shortFN.endsWith(".vcf")) {
      return new VCFSorter(inputFile, outputFile);
    } else if (shortFN.endsWith(".psl") || shortFN.endsWith(".pslx")) {
      return new BedSorter(inputFile, outputFile);
    } else if (shortFN.endsWith(".eqtl")) {
      return new EQTLSorter(inputFile, outputFile);
    } else if (shortFN.endsWith(".snp")) {
      return new GenericSorter(inputFile, outputFile, 1, 2);
    } else if (GWASParser.isGWASFile(shortFN)) {
      return new GWASSorter(inputFile, outputFile);
    } else if (MUTCodec.isMutationAnnotationFile(
        new ResourceLocator(inputFile.getAbsolutePath()))) {
      return new MUTSorter(inputFile, outputFile);
    } else if (shortFN.endsWith(".interaction")) {
      return new InteractionSorter(inputFile, outputFile);
    } else if (shortFN.endsWith(".bam")) {
      return new BAMSorter(inputFile, outputFile);
    } else {
      log.error("Unknown file type or sorting not supported for: " + inputFile.getName());
      return null;
    }
  }
Example #3
0
  /**
   * Switches on various attributes of locator (mainly locator path extension and whether the
   * locator is indexed) to call the appropriate loading method.
   *
   * @param locator
   * @param genome
   * @return
   */
  public List<Track> load(ResourceLocator locator, Genome genome) throws DataLoadException {

    final String path = locator.getPath().trim();
    log.info("Loading resource, path " + path);
    try {
      String typeString = locator.getTypeString();

      if (typeString.endsWith(".tbi")) {
        MessageUtils.showMessage(
            "<html><b>Error:</b>File type '.tbi' is not recognized.  If this is a 'tabix' index <br>"
                + " load the associated gzipped file, which should have an extension of '.gz'");
      }

      // This list will hold all new tracks created for this locator
      List<Track> newTracks = new ArrayList<Track>();

      String dbUrl = locator.getDBUrl();
      LoadHandler handler = getTrackLoaderHandler(typeString);
      if (dbUrl != null) {
        this.loadFromDatabase(locator, newTracks, genome);
      } else if (typeString.endsWith(".dbxml")) {
        loadFromDBProfile(locator, newTracks);
      } else if (typeString.endsWith(".gmt")) {
        loadGMT(locator);
      } else if (typeString.equals("das")) {
        loadDASResource(locator, newTracks);
      } else if (typeString.endsWith(".vcf.list")) {
        loadVCFListFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".trio")) {
        loadTrioData(locator);
      } else if (typeString.endsWith("varlist")) {
        VariantListManager.loadVariants(locator);
      } else if (typeString.endsWith("samplepathmap")) {
        VariantListManager.loadSamplePathMap(locator);
      } else if (typeString.endsWith(".rnai.gct")) {
        loadRnaiGctFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".gct")
          || typeString.endsWith("res")
          || typeString.endsWith("tab")) {
        loadGctFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".gbk") || typeString.endsWith(".gb")) {
        loadGbkFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".cn")
          || typeString.endsWith(".xcn")
          || typeString.endsWith(".snp")
          || typeString.endsWith(".igv")
          || typeString.endsWith(".loh")) {
        loadIGVFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".cbs")
          || typeString.endsWith(".seg")
          || typeString.endsWith("glad")
          || typeString.endsWith("birdseye_canary_calls")
          || typeString.endsWith(".seg.zip")) {
        loadSegFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".gistic")) {
        loadGisticFile(locator, newTracks);
      } else if (typeString.endsWith(".gs")) {
        loadRNAiGeneScoreFile(locator, newTracks, RNAIGeneScoreParser.Type.GENE_SCORE, genome);
      } else if (typeString.endsWith(".riger")) {
        loadRNAiGeneScoreFile(locator, newTracks, RNAIGeneScoreParser.Type.POOLED, genome);
      } else if (typeString.endsWith(".hp")) {
        loadRNAiHPScoreFile(locator);
      } else if (typeString.contains(".tabblastn") || typeString.endsWith(".orthologs")) {
        loadSyntentyMapping(locator, newTracks);
      } else if (typeString.endsWith(".sam")
          || typeString.endsWith(".bam")
          || typeString.endsWith(".cram")
          || typeString.endsWith(".sam.list")
          || typeString.endsWith(".bam.list")
          || typeString.endsWith(".aligned")
          || typeString.endsWith(".sai")
          || typeString.endsWith(".bai")
          || typeString.equals("alist")
          || typeString.equals(Ga4ghAPIHelper.RESOURCE_TYPE)) {
        loadAlignmentsTrack(locator, newTracks, genome);
      } else if (typeString.endsWith(".wig")
          || typeString.endsWith(".bedgraph")
          || typeString.endsWith(".bdg")
          || typeString.endsWith("cpg.txt")
          || typeString.endsWith(".expr")) {
        loadWigFile(locator, newTracks, genome);
      } else if (typeString.endsWith("fpkm_tracking")
          || typeString.endsWith("gene_exp.diff")
          || typeString.endsWith("cds_exp.diff")) {
        loadCufflinksFile(locator, newTracks, genome);
      } else if (typeString.contains(".dranger")) {
        loadDRangerFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".ewig.tdf") || (typeString.endsWith(".ewig.ibf"))) {
        loadEwigIBFFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".bw")
          || typeString.endsWith(".bb")
          || typeString.endsWith(".bigwig")
          || typeString.endsWith(".bigbed")) {
        loadBWFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".ibf") || typeString.endsWith(".tdf")) {
        loadTDFFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".counts")) {
        loadGobyCountsArchive(locator, newTracks, genome);
      } else if (WiggleParser.isWiggle(locator)) {
        loadWigFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".maf")) {
        loadMultipleAlignmentTrack(locator, newTracks, genome);
      } else if (typeString.endsWith(".maf.dict")) {
        loadMultipleAlignmentTrack(locator, newTracks, genome);
      } else if (typeString.contains(".peak.bin")) {
        loadPeakTrack(locator, newTracks, genome);
      } else if (typeString.endsWith("mage-tab")
          || ExpressionFileParser.parsableMAGE_TAB(locator)) {
        locator.setDescription("MAGE_TAB");
        loadGctFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".bp")) {
        loadBasePairFile(locator, newTracks, genome);
      } else if (GWASParser.isGWASFile(typeString)) {
        loadGWASFile(locator, newTracks, genome);
      } else if (GobyAlignmentQueryReader.supportsFileType(path)) {
        loadAlignmentsTrack(locator, newTracks, genome);
      } else if (typeString.endsWith(".list")) {
        // This should be deprecated
        loadListFile(locator, newTracks, genome);
      } else if (typeString.endsWith(".smap")) {
        loadSMAPFile(locator, newTracks, genome);
      } else if (CodecFactory.hasCodec(locator, genome) && !forceNotTribble(typeString)) {
        loadTribbleFile(locator, newTracks, genome);
      } else if (handler != null) {
        // Custom loader specified
        log.info(String.format("Loading %s with %s", path, handler));
        handler.load(path, newTracks);
      } else if (AttributeManager.isSampleInfoFile(locator)) {
        // This might be a sample information file.
        AttributeManager.getInstance().loadSampleInfo(locator);
      } else {
        MessageUtils.showMessage("<html>Unknown file type: " + path + "<br>Check file extension");
      }

      // Track line
      TrackProperties tp = null;
      String trackLine = locator.getTrackLine();
      if (trackLine != null) {
        tp = new TrackProperties();
        ParsingUtils.parseTrackLine(trackLine, tp);
      }

      for (Track track : newTracks) {

        if (locator.getFeatureInfoURL() != null) {
          track.setUrl(locator.getFeatureInfoURL());
        }
        if (tp != null) {
          track.setProperties(tp);
        }
        if (locator.getColor() != null) {
          track.setColor(locator.getColor());
        }
        if (locator.getSampleId() != null) {
          track.setSampleId(locator.getSampleId());
        }
      }

      return newTracks;
    } catch (Exception e) {
      if (!NOLogExceptions.contains(e.getClass())) {
        log.error(e.getMessage(), e);
      }
      throw new DataLoadException(e.getMessage());
    }
  }