[Biojava-l] GenBank Parser Error

Cox, Greg gcox@netgenics.com
Mon, 12 Feb 2001 11:41:14 -0500

Sorry about you getting two copies Simon, I hit reply instead of reply to
all, and then I realized other people might want the response.

This looks like a different flavor of the remote location problem that
cropped up last week.  There's no quick fix for it, and it's not at all
clear that there's a long, drawn out fix that will make everyone happy.  Is
this something you need now, or can you work around it?  

	By the way, what version of the parser are you using?


-----Original Message-----
From: Simon Foote [mailto:foote@nrcbsa.bio.nrc.ca]
Sent: Monday, February 12, 2001 11:22 AM
To: biojava-l@biojava.org
Subject: [Biojava-l] GenBank Parser Error


I have stumbled across an error with the GenBank parser.  If the 
location string for a gene is similar to the following:

gene           order(AF084223.1:1..265,1..245)

It will  give a bad locator error.  (Test with Genbank Accession AF084223)
I know the version being in the parantheses is causing the problem, but 
haven't figured out an easy way to correct this yet.
Anyone have a quick fix for this.


Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-991-4342  [F] 613-952-9092

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