[Bioperl-l] New feature "Bond"

[tex at ix.netcom.com]

Hilmar,

The only documentation on the bond feature that I could find is here:

http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/SEQLOC.HTML

It's a subpage of the NCBI's IEB SDK ToolBox documentation (try saying that five times fast). Hope that this helps.

Tex Thompson
RIT Bioinformatics Department

-------Original Message-------
From: Hilmar Lapp <hlapp at gnf.org>
Sent: 05/27/03 02:06 PM
To: Jason Stajich <jason at cgt.duhs.duke.edu>, "M K. Govind" <mk_govind at rediffmail.com>
Subject: RE: [Bioperl-l] New feature  "Bond"

> 
> My problem also has been that I can't find the bond() operator mentioned
in the official Genbank feature table definition. Until someone
convinces me that this is officially sanctioned Genbank notation I'm not
particularly eager to turn the Location model upside down.

Just bailing out with an exception of course isn't very nice either...

   	-hilmar

> -----Original Message-----
> From: Jason Stajich [mailto:jason at cgt.duhs.duke.edu] 
> Sent: Tuesday, May 27, 2003 6:22 AM
> To: M K. Govind
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] New feature "Bond"
> 
> 
> There are report about this (#1043, #1371 at 
> bugzilla.bioperl.org) - but apparently no one has gotten 
> around to applying any fixes for it if you still see them.
> 
> Perhaps someone will volunteer to fix this.  To do it 
> properly so that we can actually write out a 'bond' operator 
> will take some work to the Bioperl location object model 
> because we currently don't handle the operator.  Aaron's fix 
> posted in #1371 skips the feature all together - which is 
> better than falling over, but of course loses that information.
> 
> 
> -jason
> 
> On Tue, 27 May 2003, M K. Govind wrote:
> 
> > Dear all
> >
> > I am finding a new feature called "bond" in a few genbank 
> files. And 
> > the program refuses to parse and returns an error "operator bond" 
> > unrecognised by the parser
> >
> > HOw do i resolve this and parse this feature as well ?
> >
> > Thank you
> >
> > -Govind
> > ___________________________________________________
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> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu 
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