[Biojava-l] Exception when reading protein fasta file

[Ren, Zhen]

Hi,

What's wrong with the code below when testing with a file containing this sequence in FASTA format?

 >AAP40098 Sequence at antigenic site of a VP1 capsid protein of foot and mouth disease virus (FMDV) selected from serotypes A24 Cruzeiro, C3 Indaial or O1 BFS. 10 bp 
vhvsgnqhtl

Here is the exception message I got:

BioException: Could not read sequence
java.io.IOException: Can't reset: Mark invalid parseStart=12 bytesRead=512
        at org.biojava.bio.seq.io.FastaFormat.readSequenceData(FastaFormat.java:173)
        at org.biojava.bio.seq.io.FastaFormat.readSequence(FastaFormat.java:123)
        at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:100)
rethrown as org.biojava.bio.BioException: Could not read sequence
        at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:103)
        at CTerm.computeLength(CTerm.java:61)
        at CTerm.run(CTerm.java:94)

The strange thing is that when you run this program against this sequence alone, it is just fine.  However, when I ran the program against a protein FASTA file containing this sequnece, the above exception always happened.  I really don't see anything special for this sequence.  The file is just plain text file.  I tried to attach the origianl file or included the whole file in this email, both have been rejected by the mailing list.  Please help!  Thanks a lot.

Zhen

code:

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

public class TestSeqIOTools {

    public static void main(String[] args) {

        if (args.length != 1) {
            System.out.println("Usage: java TestSeqIOTools filename.fasta");
            System.exit(1);
        }

        try {
            BufferedReader fin = new BufferedReader(new FileReader(args[0]));
            SequenceIterator stream = SeqIOTools.readFastaProtein(fin);
            while(stream.hasNext()) {
                Sequence seq = stream.nextSequence();
                System.out.println(seq.seqString());
            }
            fin.close();
        } catch(BioException e) {
            System.err.println("BioException: " + e.getMessage());
            e.printStackTrace();
            System.exit(0);
        } catch(IOException ex) {
            System.err.println("IOException: " + ex.getMessage());
        }
    }
}