org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader 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.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.*;
import java.util.ListIterator;

/**
 * http://www.bioperl.org/wiki/GTF
 * Read and write FeatureLists as GFF/GTF formatted files.
 *


 * The GFF moniker is applied to a variety of tab-delimited formats
 * that mock the notion of a standard. This class should parse most files
 * bearing at least a passing resemblance to any of the formats. You will, however, need
 * to research the semantics of the files you encounter. Generally,
 * the format consists of 9 tab-delimited fields:
 * 

 *  * seqname   source   featureType   start   end   score   strand   frame   attributes
 * 
 * The 9th field consists of key-value pairs separated by semicolons, the first of which JavaGene interprets
 * as the group id (as used in GFF1). It is the precise meaning of this 9th field that
 * varies from week to week. The Feature and FeatureList objects provide various utility methods to
 * ease the task of accessing and using the attributes. The proper interpretation of any
 * particular attribute, however, is left to you.
 *
 * @author Hanno Hinsch
 */
public class GeneIDGFF2Reader {

	private static final Logger logger = LoggerFactory.getLogger(GeneIDGFF2Reader.class);

	/**
	 * Read a file into a FeatureList. Each line of the file becomes one Feature object.
	 *
	 * @param filename The path to the GFF file.
	 * @return A FeatureList.
	 * @throws IOException Something went wrong -- check exception detail message.
	 */
	public static FeatureList read(String filename) throws IOException {
		logger.info("Reading: {}", filename);

		FeatureList features = new FeatureList();
		BufferedReader br = new BufferedReader(new FileReader(filename));

		String s;
		for (s = br.readLine(); null != s; s = br.readLine()) {
			s = s.trim();

			if (s.length() > 0) {
				if (s.charAt(0) == '#') {
					//ignore comment lines
				} else {

					FeatureI f = parseLine(s);
					if (f != null) {
						features.add(f);
					}
				}
			}

		}

		br.close();
		return features;
	}

	/**
	 * create Feature from line of GFF file
	 */
	private static Feature parseLine(String s) {
		//FIXME update to use regex split on tabs
		//FIXME better errors on parse failures

		int start = 0;
		int end = 0;

		start = end;
		end = s.indexOf('\t', start);
		String seqname = s.substring(start, end).trim();

		start = end + 1;
		end = s.indexOf('\t', start);
		String source = s.substring(start, end).trim();

		start = end + 1;
		end = s.indexOf('\t', start);
		String type = s.substring(start, end);

		start = end + 1;
		end = s.indexOf('\t', start);
		String locStart = s.substring(start, end);

		start = end + 1;
		end = s.indexOf('\t', start);
		String locEnd = s.substring(start, end);

		Double score;
		start = end + 1;
		end = s.indexOf('\t', start);
		try {
			score = Double.parseDouble(s.substring(start, end));
		} catch (Exception e) {
			score = 0.0;
		}

		start = end + 1;
		end = s.indexOf('\t', start);
		char strand = s.charAt(end - 1);

		Location location = Location.fromBio(Integer.parseInt(locStart), Integer.parseInt(locEnd), strand);

		assert (strand == '-') == location.isNegative();

		int frame;
		start = end + 1;
		end = s.indexOf('\t', start);
		try {
			frame = Integer.parseInt(s.substring(start, end));
		} catch (Exception e) {
			frame = -1;
		}

		//grab everything until end of line (or # comment)
		start = end + 1;
		end = s.indexOf('#', start);
		String attributes = null;
		if (end < 0) {
			attributes = new String(s.substring(start));
		} else {
			attributes = new String(s.substring(start, end));
		}
		//need to add in attribute assignment for geneid where it just provides a gene name and will make it gtf like
		attributes = "gene_id " + '"' + attributes + '"' + ";";
		return new Feature(seqname, source, type, location, score, frame, attributes);

	}

	/**
	 * Write features in FeatureList to file. Each Feature becomes one line in the file.
	 * The userMap() data in the features is not written to file.
	 *
	 * @param features The list of features to write.
	 * @param filename The path to the file.
	 * @throws IOException Something went wrong -- check exception detail message.
	 */
	public static void write(FeatureList features, String filename) throws IOException {
		logger.info("Writing: {}", filename);

		BufferedWriter bw = new BufferedWriter(new FileWriter(filename));

		ListIterator iter = features.listIterator();
		while (iter.hasNext()) {
			Feature feature = (Feature) iter.next();
			writeLine(feature, bw);
		}

		bw.close();
	}

	private static void writeLine(Feature f, BufferedWriter bw) throws IOException {
		String s = f.seqname() + '\t';
		s += f.source() + '\t';
		s += f.type() + '\t';

		s += f.location().bioStart() + "\t";
		s += f.location().bioEnd() + "\t";
		s += Double.toString(f.score()) + "\t";
		s += f.location().bioStrand() + "\t";

		if (f.frame() == -1) {
			s += ".\t";
		} else {
			s += f.frame() + "\t";
		}

		s += f.attributes();

		bw.write(s);
		bw.newLine();
	}


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

		FeatureList listGenes = GeneIDGFF2Reader.read("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/genemark_hmm.gtf");

		for(FeatureI feature : listGenes){
			logger.info("Gene Feature: {}", feature);
		}
//        logger.info(listGenes);
		//	GeneMarkGTF.write( list, args[1] );
	}
}