Examples of GFFCodec

org.broad.igv.feature.tribble.GFFCodec
equenceontology.org/gff3.shtml These tags have predefined meanings (tags are case sensitive):
ID Indicates the name of the feature (unique). Name Display name for the feature. Alias A secondary name for the feature. Parent Indicates the parent of the feature.
Specs: GFF3 http://www.sequenceontology.org/gff3.shtml GFF2 specification: http://www.sanger.ac.uk/resources/software/gff/spec.html UCSC GFF (GFF "1") http://genome.ucsc.edu/FAQ/FAQformat#format3 GTF http://mblab.wustl.edu/GTF2.html UCSC GTF http://genome.ucsc.edu/FAQ/FAQformat#format4 Feature type definitions http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.2

Examples of org.broad.igv.feature.tribble.GFFCodec


        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);

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Examples of org.broad.igv.feature.tribble.GFFCodec

 * @author jacob
 * @date 2013-Apr-29
 */
public class CufflinksTranscriptDecoder extends RenameDecoder{
    public CufflinksTranscriptDecoder() {
        super(new GFFCodec(GenomeManager.getInstance().getCurrentGenome()));
    }

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Examples of org.broad.igv.feature.tribble.GFFCodec

    }


    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");
        }

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Examples of org.broad.igv.feature.tribble.GFFCodec

    static Logger log = Logger.getLogger(GFFParser.class);


    private TrackProperties trackProperties = null;


    public List<htsjdk.tribble.Feature> loadFeatures(BufferedReader reader, Genome genome) {
        return loadFeatures(reader, genome, new GFFCodec(genome));
    }

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Examples of org.broad.igv.feature.tribble.GFFCodec

        try {
            Genome genome = null; // Not needed for this test
            gffReader = new BufferedReader(new FileReader(inputFile));
            GFFParser parser = new GFFParser();
            GFFCodec.Version version = inputFile.getPath().endsWith(".gff3") ? GFFCodec.Version.GFF3 : GFFCodec.Version.GFF2;
            GFFCodec codec = new GFFCodec(version, null);
            List<Feature> gffFeatures = parser.loadFeatures(gffReader, genome, codec);


            bedReader = new BufferedReader(new FileReader(outputFile));
            FeatureParser bedParser = AbstractFeatureParser.getInstanceFor(new ResourceLocator(outputFile.getAbsolutePath()), null);
            List<Feature> bedFeatures = bedParser.loadFeatures(bedReader, genome);

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