Examples of GFFParser

Examples of org.biojava.bio.program.gff.GFFParser

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        // have to and the filters together
        GFFAndFilter aFilter = new GFFAndFilter(fFilter, sFilter);
        GFFFilterer filterer = new GFFFilterer(gffEntries.getAddHandler(), aFilter);

        // parse the gff file
        GFFParser parser = new GFFParser();
        parser.parse(new BufferedReader(new InputStreamReader(new FileInputStream(new File(gffFileName)))), filterer);

        // find all of the features
        // output to the out file the tube information
        //outFile = new PrintWriter(new BufferedWriter(new FileWriter(outFileName)));
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Examples of org.broad.igv.feature.GFFParser

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public class GFFtoBed {


    public static void convert(File inputFile, File outputFile) {

        GFFParser parser = new GFFParser();

        BufferedReader reader = null;
        PrintWriter pw = null;
        try {
            GFFCodec.Version version = inputFile.getPath().endsWith(".gff3") ? GFFCodec.Version.GFF3 : GFFCodec.Version.GFF2;
            GFFCodec gffCodec = new GFFCodec(version, null);
            reader = ParsingUtils.openBufferedReader(new ResourceLocator(inputFile.getAbsolutePath()));
            List<Feature> features = parser.loadFeatures(reader, null, gffCodec);

            IGVBEDCodec codec = new IGVBEDCodec();
            codec.setGffTags(true);

            pw = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));
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Examples of org.broad.igv.feature.GFFParser

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        }
    }

    private void GFFToBed(String ifile, String ofile) throws FileNotFoundException{
        IGVBEDCodec outCodec = new IGVBEDCodec();
        GFFParser parser = new GFFParser();
        GFFCodec codec = null;
        try {
            codec = (GFFCodec) CodecFactory.getCodec(ifile, null);
        } catch (Exception e) {
            throw new IllegalArgumentException("Input file is not recognized as a GFF");
        }
        BufferedReader reader = null;
        PrintStream outStream = System.out;
        if(!ofile.equals(STDOUT_FILE_STR)){
            outStream = new PrintStream(new FileOutputStream(ofile));
        }
        try {
            reader = ParsingUtils.openBufferedReader(ifile);
            List<Feature> features = parser.loadFeatures(reader, null, codec);
            for (Feature feat : features) {
                String encoded = outCodec.encode(feat);
                outStream.print(encoded);
                outStream.print('\n');
            }
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