[Biojava-l] Parse error with negative strand CDS

[Schreiber, Mark]

The problem appears to be in the way that VNTI represents the coordinates of locations that cross the origin of a circular molecule. It is not done in the "NCBI way" so the parser gets a little confused. I think we can make the parser more tolerant but we need to sort out a few issues in the deep dark bowels of biojava seqio first.
 
- Mark
 

	-----Original Message----- 
	From: Peter Wilkinson [mailto:pwilkinson at videotron.ca] 
	Sent: Sat 13/09/2003 1:38 a.m. 
	To: Schreiber, Mark; Criscuolo, Fred; biojava-l at biojava.org 
	Cc: 
	Subject: RE: [Biojava-l] Parse error with negative strand CDS
	
	

	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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