[Biojava-l] writesequence problem

[Stein Aerts]

Hello,
There appears to be a problem when writing a sequence to file in EMBL
format, but only if it contains a multiple of 60 nucleotides (there are 60
nt's on each line): the last line of nucleotides is not written and the
nucleotide-count of the last line is incorrect.

Example code below and example sequence files in attachment.

Best regards,
Stein Aerts.

________________________________________

import org.biojava.bio.seq.io.*;
import org.biojava.bio.seq.*;
import java.io.*;

public class TestEmbl {


  public static void main(String[] args) throws Exception {
    Sequence seq = null;
    BufferedReader br = new BufferedReader(new
FileReader("D:\\SAE\\temp\\test_in.embl"));
    SequenceIterator stream = SeqIOTools.readEmbl(br);
    if (stream.hasNext()){
      seq = stream.nextSequence();
    }
    SequenceFormat format = new EmblLikeFormat();
    OutputStream out = new FileOutputStream("D:\\SAE\\temp\\test_out.embl");
    format.writeSequence(seq, new PrintStream(out));
  }
}

test_out.embl
Description: Binary data

test_in.embl
Description: Binary data