[Biojava-l] Parse error with negative strand CDS

[Peter Wilkinson]

Well ... Fred.

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:fred.criscuolo at pfizer.com]
>Sent: Friday, 12 September 2003 4:27 a.m.
>To: 'biojava-l at biojava.org'
>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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-------------------------------------
Peter Wilkinson
Bioinformatics Consultant

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