Having worked for the company that makes VectorNTI (Informax), I can tell you that there are some modifications to the format that should be benign ... but that is not always true. The output of GenBank files from VectorNTI are slightly different, but Iwould not have expected them to break the parser.
the annotations within VectorNTI are added into the comments fields, which should not be a problem.
One thing to check is whether biojava parser is updated to the current genbank format, and whether the output from vectorNTI produces the same 'version' of the genbank file. If they don't then the biojava parser may not handle the vectorNTI output.
if you could send the file I can see what the problem is, the line on its own does not seem like a problem. It might be some spacing issues (version of the formatting) in the file generated on the previous line somewhere.
Peter
At 10:04 AM 12/09/2003 +1200, Schreiber, Mark wrote:
Hi -
This looks odd. It may be that the Genbank produced by VectorNTI is not quite right. Can you post the file, or at least the few lines surrounding the CDS feature?
- Mark
-----Original Message----- From: Criscuolo, Fred [mailto:[EMAIL PROTECTED] Sent: Friday, 12 September 2003 4:27 a.m. To: '[EMAIL PROTECTED]' Subject: [Biojava-l] Parse error with negative strand CDS
Hi,
I am using BioJava 1.3.0 to process a GenBank file that has a CDS on the negative strand. I am using the SeqIOTools.readGenbank(BufferedReader)
method to parse the file. I get the following error for any CDS on the negative strand:
This line could not be parsed: CDS complement(518..1597)
The GenBank files I'm working with are produced by the VectorNTI application. I'm using Java 1.4.2. I've searched the biojava mailing list but have not seen a reference to this particular problem. Any idea what's wrong? Thanks. Fred
Fred Criscuolo Research Informatics - Pfizer, Inc. 858.622.7307
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