[Biojava-l] Parsing location from gbk files

[charles.girardot@libertysurf.fr]

Hi,

I am using biojava to extract mRNA, CDS and gene boundaries from genbank annotation files (e.g., "hs_chr19.gbs" from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/).
I've just switched from the biojava 1.22 to latest 1.3 release (biojava-1.30-jdk14.jar and bytecode-0.92.jar) 
and I get lots of exception (see below, the peace of code generating this follows as well). Don't known if it's important but ".gbs" files do not hold the contig sequences but only annotations.

Nota: I am using the jdk 1.4.1.

Thanks for your help.

Charles Girardot


=======================================
java.lang.IllegalArgumentException: Location 59817 is outside 1..0
	at org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:306)
	at org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature.java:74)
	at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:274)
	at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138)
rethrown as org.biojava.bio.BioException: Couldn't realize feature
	at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144)
	at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94)
	at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198)
	at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204)
	at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168)
	at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87)
	at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98)
	at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101)
	at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34)
	


==========================================

package org.gc.test;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;

import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.io.SeqIOTools;

/**
 * @author unknown
 *
 * To change the template for this generated type comment go to
 * Window&gt;Preferences&gt;Java&gt;Code Generation&gt;Code and Comments
 */
public class GenbankParserTest {

public static void main(String[] args) {
System.out.println("Main starts ...");
	try {

	File f = new File("D:\\Travail\\data\\Hs_chr19.gbs");
	BufferedReader bf = new BufferedReader(new FileReader(f));
	SequenceIterator it = SeqIOTools.readGenbank(bf);
	while (it.hasNext()) {
		System.out.println("getting next seq...");
		Sequence s = it.nextSequence();
	}
	} catch (Exception e) {
		System.out.println(e.getStackTrace());
	}
System.out.println("End of main");
}
}


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