[Biojava-l] Parsing location from gbk files

Schreiber, Mark mark.schreiber at agresearch.co.nz
Wed Sep 10 17:44:04 EDT 2003

Hi -
This is a recurring problem as more files are being deposited that contain only references to other contigs but contain annotation and features.
A model where a DummySequence of appropriate length is instantiated if the contig files are not available may be useful. Possibley a GBS parser would be useful? Has anyone hacked out something like this?
- Mark

	-----Original Message----- 
	From: charles.girardot at libertysurf.fr [mailto:charles.girardot at libertysurf.fr] 
	Sent: Thu 11/09/2003 6:13 a.m. 
	To: biojava-l 
	Subject: [Biojava-l] Parsing location from gbk files

	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("End of main");
	********** L'ADSL A 20 EUR/MOIS**********
	Avec Tiscali, l'ADSL est à 20 EUR/mois. Vous pourrez chercher longtemps avant de trouver moins cher !
	Pour profiter de cette offre exceptionnelle, cliquez ici : http://register.tiscali.fr/adsl/
	Offre soumise à conditions.
	Biojava-l mailing list  -  Biojava-l at biojava.org

Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.

More information about the Biojava-l mailing list