org.biojava.nbio.genome.parsers.gff.GFF3Writer Maven / Gradle / Ivy

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/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.genome.parsers.gff;

import org.biojava.nbio.genome.GeneFeatureHelper;
import org.biojava.nbio.core.sequence.*;

import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedHashMap;

/**
 *
 * @author Scooter Willis 
 */
public class GFF3Writer {

	/**
	 * Output gff3 format for a DNA Sequence
	 * @param fileName
	 * @param chromosomeSequence
	 * @throws Exception
	 */
	public void write(OutputStream outputStream, LinkedHashMap chromosomeSequenceList) throws Exception {

		outputStream.write("##gff-version 3\n".getBytes());
		for (String key : chromosomeSequenceList.keySet()) {
			ChromosomeSequence chromosomeSequence = chromosomeSequenceList.get(key);
			String gff3line = "";
	//         if(source.length() == 0){
	//             Collection genes = chromosomeSequence.getGeneSequences().values();
	//             for(GeneSequence gene : genes){
	//                 source = gene.getSource();
	//                 break;
	//             }
	//         }
	//         gff3line = key + "\t" + source + "\t" + "size" + "\t" + "1" + "\t" + chromosomeSequence.getBioEnd() + "\t.\t.\t.\tName=" + key + "\r\n";
	//         outputStream.write(gff3line.getBytes());

			for (GeneSequence geneSequence : chromosomeSequence.getGeneSequences().values()) {
				gff3line = key + "\t" + geneSequence.getSource() + "\t" + "gene" + "\t" + geneSequence.getBioBegin() + "\t" + geneSequence.getBioEnd() + "\t";
				Double score = geneSequence.getSequenceScore();
				if (score == null) {
					gff3line = gff3line + ".\t";
				} else {
					gff3line = gff3line + score + "\t";
				}
				gff3line = gff3line + geneSequence.getStrand().getStringRepresentation() + "\t";
				gff3line = gff3line + ".\t";
				gff3line = gff3line + "ID=" + geneSequence.getAccession().getID() + ";Name=" + geneSequence.getAccession().getID();
				gff3line = gff3line + getGFF3Note(geneSequence.getNotesList());
				gff3line = gff3line + "\n";
				outputStream.write(gff3line.getBytes());

				int transcriptIndex = 0;
				for (TranscriptSequence transcriptSequence : geneSequence.getTranscripts().values()) {
					transcriptIndex++;

					gff3line = key + "\t" + transcriptSequence.getSource() + "\t" + "mRNA" + "\t" + transcriptSequence.getBioBegin() + "\t" + transcriptSequence.getBioEnd() + "\t";
					score = transcriptSequence.getSequenceScore();
					if (score == null) {
						gff3line = gff3line + ".\t";
					} else {
						gff3line = gff3line + score + "\t";
					}
					gff3line = gff3line + transcriptSequence.getStrand().getStringRepresentation() + "\t";
					gff3line = gff3line + ".\t";
					String id = geneSequence.getAccession().getID() + "." + transcriptIndex;
					gff3line = gff3line + "ID=" + id + ";Parent=" + geneSequence.getAccession().getID() + ";Name=" + id;
					gff3line = gff3line + getGFF3Note(transcriptSequence.getNotesList());

					gff3line = gff3line + "\n";
					outputStream.write(gff3line.getBytes());

					String transcriptParentName = geneSequence.getAccession().getID() + "." + transcriptIndex;
					ArrayList cdsSequenceList = new ArrayList(transcriptSequence.getCDSSequences().values());
					Collections.sort(cdsSequenceList, new SequenceComparator());
					for (CDSSequence cdsSequence : cdsSequenceList) {
						gff3line = key + "\t" + cdsSequence.getSource() + "\t" + "CDS" + "\t" + cdsSequence.getBioBegin() + "\t" + cdsSequence.getBioEnd() + "\t";
						score = cdsSequence.getSequenceScore();
						if (score == null) {
							gff3line = gff3line + ".\t";
						} else {
							gff3line = gff3line + score + "\t";
						}
						gff3line = gff3line + cdsSequence.getStrand().getStringRepresentation() + "\t";
						gff3line = gff3line + cdsSequence.getPhase() + "\t";
						gff3line = gff3line + "ID=" + cdsSequence.getAccession().getID() + ";Parent=" + transcriptParentName;
						gff3line = gff3line + getGFF3Note(cdsSequence.getNotesList());

						gff3line = gff3line + "\n";
						outputStream.write(gff3line.getBytes());
					}

				}
			}

		}


	}

	private String getGFF3Note(ArrayList notesList) {
		String notes = "";

		if (notesList.size() > 0) {
			notes = ";Note=";
			int noteindex = 1;
			for (String note : notesList) {
				notes = notes + note;
				if (noteindex < notesList.size() - 1) {
					notes = notes + " ";
				}
			}

		}
		return notes;
	}

	public static void main(String args[]) throws Exception {

		if (true) {
			FileOutputStream fo = new FileOutputStream("/Users/Scooter/scripps/dyadic/geneid/geneid/c1-geneid.gff3");//-16
			LinkedHashMap dnaSequenceList = GeneFeatureHelper.loadFastaAddGeneFeaturesFromGeneIDGFF2(new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/454Scaffolds.fna"), new File("/Users/Scooter/scripps/dyadic/geneid/geneid/c1_geneid.gff"));
			GFF3Writer gff3Writer = new GFF3Writer();
			gff3Writer.write(fo, dnaSequenceList);


	 //       LinkedHashMap proteinSequenceList = GeneFeatureHelper.getProteinSequences(chromosomeSequenceList.values());
	 //       for(String id : proteinSequenceList.keySet()){
	 //           ProteinSequence sequence = proteinSequenceList.get(id);
	 //           System.out.println(id + " " + sequence.getSequenceAsString());

	 //       }
			fo.close();
		}
/*
		if (false) {
			FileOutputStream fo = new FileOutputStream("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/genemark_hmm.gff3");//-16
			LinkedHashMap dnaSequenceList = GeneFeatureHelper.loadFastaAddGeneFeaturesFromGeneMarkGTF(new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/454Scaffolds.fna"), new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/genemark_hmm.gtf"));
			GFF3Writer gff3Writer = new GFF3Writer();
			gff3Writer.write(fo, dnaSequenceList);
			fo.close();
		}

		if (false) {
			LinkedHashMap dnaSequenceList = GeneFeatureHelper.loadFastaAddGeneFeaturesFromGlimmerGFF3(new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/454Scaffolds-16.fna"), new File("/Users/Scooter/scripps/dyadic/GlimmerHMM/c1_glimmerhmm-16.gff"));
			GFF3Writer gff3Writer = new GFF3Writer();
			gff3Writer.write(System.out, dnaSequenceList);
		}
		*/
//        System.out.println(listGenes);
		//	GeneMarkGTF.write( list, args[1] );
	}
}