[Biojava-l] bug using getFeature() ?

[Alberto Ambesi]

my program fails to get a transcript feature on human chromosome 1  
within positions: 156947999-156952998. If the search is done via web at  
ensembl.org, I find ensembl transcript CASQ1, with an exon in position:  
156948909-156949040. In many other genomic regions the program works  
well. Why is this?
thank you in advance.
dr. Alberto Ambesi

--

import java.sql.*;
import java.util.*;
import org.ensembl.db.*;
import org.ensembl.db.sql.SQLDatabaseAdaptor;
import org.biojava.bio.*;
import org.biojava.bio.program.ensembl.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;

public class bug {
     public static void main(String[] args) throws Exception {
         Driver driverName =  
(Driver)Class.forName("org.gjt.mm.mysql.Driver").newInstance();
         //Connection conn =  
DriverManager.getConnection("jdbc:mysql://kaka.sanger.ac.uk/ 
homo_sapiens_core_15_33", "anonymous", "");
         SQLDatabaseAdaptor sqlDBAdaptor =  
SQLDatabaseAdaptor.connectSQL("jdbc:mysql://kaka.sanger.ac.uk/ 
homo_sapiens_core_15_33", "anonymous", "", 9);
         Ensembl ens = new Ensembl(sqlDBAdaptor);
         SequenceDB chromosomes =ens.getChromosomes();
         Sequence chrSeq = chromosomes.getSequence("1");
         Sequence seq = new SubSequence(chrSeq, 156947999, 156952998);
         System.out.println(seq.seqString());
         for (Iterator fi = seq.features(); fi.hasNext(); ) {
             org.biojava.bio.seq.Feature f =  
(org.biojava.bio.seq.Feature) fi.next();
             String featureType = f.getType();
             System.out.println(featureType);
         }
     }
}
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