[Bioperl-l] New feature "Bond"

[Heikki Lehvaslaiho]

On Tue, 2003-05-27 at 20:06, Hilmar Lapp wrote:
> 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...

I agree.

'bond' is anomaly. We should not try to parse it unless it is officially
sanctioned by Sequence Database collaboration. Would be nice to get
parsers to ignore it...

	-Heikki

> 	-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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> > Bioperl-l at portal.open-bio.org 
> > http://portal.open-> bio.org/mailman/listinfo/bioperl-l
> > 
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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