Examples of org.broad.igv.data.expression.GeneToLocusHelper

     * @return
     */
    public static void convert(File inputFile, File outputFile, String probeResource,
                               int maxRecords, File tmpDir, Genome genome) throws IOException {


        GeneToLocusHelper locusHelper = new GeneToLocusHelper(probeResource);




        BufferedReader reader = null;
        PrintWriter writer = null;


        SortingCollection cltn = getSortingCollection(maxRecords, tmpDir);
        try {
            reader = new BufferedReader(new FileReader(inputFile));
            writer = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));


            // Parse the header line
            String headerLine = reader.readLine();
            String[] tokens = headerLine.split("\t");


            //The sample names in a GCT file start at column 2,
            int sampleStart = 2;




            String nextLine = null;
            TrackType dataType = TrackType.GENE_EXPRESSION;
            while ((nextLine = reader.readLine()) != null) {


                // A gct row can map to multiple loci, normally this indicates a problem with the probe
                DataRow row = new DataRow(nextLine);
                String probe = row.getProbe();
                if (probe.startsWith("cg")) {
                    dataType = TrackType.DNA_METHYLATION;
                }


                List<Locus> loci = locusHelper.getLoci(probe, row.getDescription(), genome.getId());
                if (loci == null || loci.isEmpty()) {
                    System.out.println("No locus found for: " + probe + "  " + row.getDescription());
                } else {
                    for (Locus locus : loci) {
                        String igvLine = locus.getChr() + "\t" + locus.getStart() + "\t" + locus.getEnd() + "\t" + probe +

    public static void convert(ResourceLocator resourceLocator, File outputFile, String probeResource,
                        int maxRecords, File tmpDir, Genome genome) throws IOException {


        ExpressionFileParser.FileType type = ExpressionFileParser.determineType(resourceLocator);


        GeneToLocusHelper locusHelper = new GeneToLocusHelper(probeResource);




        BufferedReader reader = null;
        PrintWriter writer = null;


        SortingCollection cltn = getSortingCollection(maxRecords, tmpDir);
        try {
            reader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(resourceLocator.getPath())));
            writer = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));


            ExpressionFileParser.FormatDescriptor formatDescriptor = ExpressionFileParser.parseHeader (reader, type, null);
            String [] dataHeadings = formatDescriptor.getDataHeaders();




            // Need a better way to determine type!
            String dataType = resourceLocator.getPath().contains("methylation") ? TrackType.DNA_METHYLATION.toString()
                    : TrackType.GENE_EXPRESSION.toString();


            writer.println("#type=" + dataType);
            writer.print("Chr\tStart\tEnd\tProbe");
            for (String s : dataHeadings) {
                writer.print("\t" + s);
            }
            writer.println();


            String nextLine = null;
            while ((nextLine = reader.readLine()) != null) {


                // A gct row can map to multiple loci, normally this indicates a problem with the probe
                DataRow row = new DataRow(nextLine, formatDescriptor);
                String probe = row.getProbe();
                List<Locus> loci = locusHelper.getLoci(probe, row.getDescription(), genome.getId());
                if (loci == null || loci.isEmpty()) {
                    log.warn("No locus found for: " + probe + "  " + row.getDescription());
                } else {
                    for (Locus locus : loci) {
                        String igvLine = locus.getChr() + "\t" + locus.getStart() + "\t" + locus.getEnd() + "\t" + probe +

Examples of org.broad.igv.data.expression.GeneToLocusHelper

Related Classes of org.broad.igv.data.expression.GeneToLocusHelper