[Biojava-l] Exception when reading protein fasta file

[Ren, Zhen]

Hi,

When the name of the sequence becomes shorter, the problem does disappear.  Anyway, I deleted that sequence from my input file.  The same problem happened again to another sequence which is pretty short this time.

>AAR14362 E.histolytica protein. 167 bp 
mkimkmmkmkkqvqvitqnqaqvinqiinqkqvqvinqkqvqvinqiinqkqvqvinqii
nqkqvqvinqiinqkqvqvinqiinqkqaqvinqiinqkqaqlinqkqaqlinqkqaqli
nqkqaqlinqkqaqlviqminqevvqitiiitlmlhqvhslfsvlsl

Any idea?  Thanks again.

Zhen

-----Original Message-----
From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
Sent: Thursday, October 17, 2002 3:01 PM
To: Ren, Zhen; biojava-l@biojava.org
Subject: RE: [Biojava-l] Exception when reading protein fasta file


Hi -

I suspect what is happening is the name of the file is too long for the
read ahead facility of the inputstream. When you mark a point on a
stream you can only read ahead a certain distance before the mark is
lost. I'll see if I can fix it. The temporary solution is to trim the
fasta header to a smaller size.

- Mark


> -----Original Message-----
> From: Ren, Zhen [mailto:zren@amylin.com] 
> Sent: Friday, 18 October 2002 10:22 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Exception when reading protein fasta file
> 
> 
> 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(FastaForma
> t.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());
>         }
>     }
> }
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 
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