[Biojava-l] BioException from SeqIOTools

[Schreiber, Mark]

There was also a bug with fasta description lines being very long, I'm not sure if that one got sorted or not. If there are some very long description lines try truncating them. A bit of a hack I know. Do any of the BJ gurus know the status of this bug?
 
- Mark
 

	-----Original Message----- 
	From: Ren, Zhen [mailto:zren at amylin.com] 
	Sent: Wed 9/04/2003 11:59 a.m. 
	To: Schreiber, Mark; biojava-l at biojava.org 
	Cc: 
	Subject: RE: [Biojava-l] BioException from SeqIOTools
	
	

	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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