[Biojava-l] Embl parser problem

[mark.schreiber at novartis.com]

Hi -

A BioException would be expected when parsing an embl file via the genbank 
option. I is surprising you don't get one when parsing a genbank file via 
the embl option although it clearly has not worked properly.

You should only ever parse a file with the appropriate read method.

Please note that if you have access to CVS you could download the 
development version of the new parsers (biojavax) which do a much better 
job.

- Mark





"Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent by: biojava-l-bounces at portal.open-bio.org
01/03/2006 10:21 PM

 
        To:     <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Embl parser problem


Hi,

 

I have an application using BioJava1.4pre1.4 that loads an embl or
genbank file.

 

If I load an embl file via the genbank option a BioException error is
thrown.

 

But if I load a genbank file via the embl option no BioException is
thrown and the sequence is created although it is not correct e.g.
sequence.length() returns 0

 

An example of code using the sequence file from the BioJava demos

 

String fileName =
"C:/Downloads/Java/BioJava/BioJava-1.4pre1/biojava-1.4pre1/demos/seq/AL1
21903.genbank"; 

try {

  seq = SeqIOTools.readEmbl(new BufferedReader(new
FileReader(fileName))).nextSequence();

  System.out.println("URN: " + seq.getURN());

  System.out.println("Length: " + seq.length());

}

catch (BioException BIOE) {

  System.out.println("BioException " + BIOE);

}

 

The output is:

URN: sequence/embl:SION

Length: 0

 

If I use the matching embl sequence from the demos the output is:

URN: sequence/embl:AL121903

Length: 80600

 

I've used BioJava1.4 with the same outcome. Should I be parsing the file
an alternative way?

 

Thanks,

 

Jolyon

 


_______________________________________________
Biojava-l mailing list  -  Biojava-l at biojava.org
http://biojava.org/mailman/listinfo/biojava-l