[Biojava-l] BioException from SeqIOTools

[Ren, Zhen]

I compiled JAR files using the latest code through cvs and the latest JDKs including 1.4.1_01, 1.4.1_02 and 1.4.2_beta all have the same problem.  Any other thought? Thanks.  -Zhen

-----Original Message-----
From: Schreiber, Mark [mailto:mark.schreiber at agresearch.co.nz]
Sent: Tuesday, April 08, 2003 4:45 PM
To: Ren, Zhen; biojava-l at biojava.org
Subject: RE: [Biojava-l] BioException from SeqIOTools


Hi -
 
This sort of thing used to show up on large files with earlier versions of biojava. What version are you using?
 
- Mark
 

	-----Original Message----- 
	From: Ren, Zhen [mailto:zren at amylin.com] 
	Sent: Wed 9/04/2003 5:01 a.m. 
	To: biojava-l at biojava.org 
	Cc: 
	Subject: [Biojava-l] BioException from SeqIOTools
	
	

	Hi, there,
	
	Can anyone tell me what is wrong in the following snippet?  I can not attach you my troubling big FASTA file with lots of protein sequences in it.  When the problematic sequence is extracted from the file, the exception disappears.  Thanks so much.
	
	Zhen
	
	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.getName());
	                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());
	        }
	    }
	}
	
	C:\Biojava\trouble>javac TestSeqIOTools.java
	
	C:\Biojava\trouble>java TestSeqIOTools mySeqs.fasta
	......
	>AAY11855;
	MTRECPSPAPGPGAPLSGSVLAEAAVVFAVVLSIHATVW
	BioException: Could not read sequence
	java.io.IOException: Can't reset: Mark invalid parseStart=89 bytesRead=512
	        at org.biojava.bio.seq.io.FastaFormat.readSequenceData(FastaFormat.java:170)
	        at org.biojava.bio.seq.io.FastaFormat.readSequence(FastaFormat.java:120)
	        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 TestSeqIOTools.main(TestSeqIOTools.java:19)
	
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