I have found 2 realated problems.
System:
biojava 1.10
Both Unix and DOS both running jdk1.3
If I read a file in genbank format that has DOS endings and try to iterate
through the SequenceIterator
sI1 = SeqIOTools.readGenbank(br1);
while(sI1.hasNext()){
seq = sI1.nextSequence();
.....
}
It gets the one sequence that the file contains then the nextSequence method
chokes on the second pass.
Exception in thread "main" java.io.IOException: Premature end of
stream for GENBANK
at
org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java:112)
at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:99)
rethrown as org.biojava.bio.BioException: Could not read sequence
at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102)
at GenbankTest.main(GenbankTest.java:39)
the same genbank file with Unix line endings has no problem. True on both
Unix and DOS
You might ask why I was doing this since the file only had one file in it.
Well I really wasn't, but StreamWriter does. This is where the problem
really comes in. StreamWriter wraps the nextSequence call in a try block
inside a while hasNext loop.
so passing a SequenceIterator that chokes in the middle as above to
StreamWriter is equivalent to:
while (seqI.hasNext()){
try{
seq1 = seqI.nextSequence(); //choke here
}catch (Exception
System.out.println(e.getMessage());
}
}
OOOPS the try keeps hasNext from returning false -- this takes a good long
while on my machine.
Finally just wondering what the plans are for implementing writeSequence for
Genbank?
David
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| David Waring
| Systems Programmer
| University of Washington Genome Center
| [EMAIL PROTECTED]
| (206) 221-6902
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