[Biojava-l] FASTA reader problem: "Mark invalid"

[Christian Gruber]

Hi!

I wrote a Java test program that just reads in a sequence in FASTA
format and prints the sequences out. I did this by making the
appropriate changes to the file demos/seq/TestEmbl.java. As a test
sequence file in FASTA format, i created one with random sequences.

Now the problem: There are some sequence files that are definitely
correct FASTA format files, but create the following error message:


---------------------------------------------


java.io.IOException: Mark invalid
        at java.lang.Throwable.<init>(Throwable.java:96)
        at java.lang.Exception.<init>(Exception.java:44)
        at java.io.IOException.<init>(IOException.java:49)
        at java.io.BufferedReader.reset(BufferedReader.java:473)
        at org.biojava.bio.seq.io.FastaFormat.readSequence(FastaFormat.java(Comp
iled Code))
        at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:88
)
rethrown as org.biojava.bio.BioException: Could not read sequence
        at java.lang.Throwable.<init>(Throwable.java:96)
        at java.lang.Exception.<init>(Exception.java:44)
        at org.biojava.bio.BioException.<init>(BioException.java:58)
        at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:90
)
        at TestFasta.main(TestFasta.java:29)



----------------------------------------------



The error always occurs reproducibly at the same location in the
file, but not with any FASTA file.


When anyone is interested in a FASTA file that creates this error, I
can send it (including my Java program source). It's ~15kb
altogether. Just send an email (Christian.Gruber@biomax.de).


Does anybody know what happens here?


Christian Gruber