[Bioperl-l] Genbank/EMBL output

[Alex Hudek]

I'm using Bioperl to export annotation information. I don't use Genbank
format myself, however a reviewer of a paper on the annotation system
requested Genbank format. According to this reviewer the form 

complement(join(...))

is more common and accepted. So I thought it wouldn't hurt to check to see
if it was possible to implement. Since major changes would be required to
incorporate such a feature into Bioperl it doesn't seem to be worth it
though. So long as the output file is valid I think it will be fine the
way it is. 

Thanks.

Alex

On Mon, 23 Dec 2002, Hilmar Lapp wrote:

> It's possible but would require a number of hacks to circumvent the 
> semantics of the object model. Those semantics define that a split 
> location does not carry strand information. It's the individual 
> locations that hold the strand instead. What you're asking for is logic 
> that checks whether all sub-locations are on the negative strand, and 
> if so promote the complement() operator to the join.
> 
> Why do you need the other form?
> 
> 	-hilmar
> 
> On Monday, December 23, 2002, at 02:04  PM, Alex Hudek wrote:
> 
> >
> > Is it possible to have bioperl output features in Genbank format of the
> > form
> >
> > complement(join(1..50,60..100))
> >
> > rather than
> >
> > join(complement(1..50),complement(60..100)) ?
> >
> > I understand the former form is more common/accepted?
> >
> >
> > Alexander K. Hudek
> > The Hospital for Sick Children
> > Room 9107, The Centre for Applied Genomics
> > 555 University Avenue
> > Toronto, Ontario, M5G 1X8, Canada
> > Lab phone: 416-813-7638
> > Fax: 416-813-8319
> > E-mail: alex@genet.sickkids.on.ca
> >
> >
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 


Alexander K. Hudek
The Hospital for Sick Children
Room 9107, The Centre for Applied Genomics
555 University Avenue
Toronto, Ontario, M5G 1X8, Canada
Lab phone: 416-813-7638
Fax: 416-813-8319
E-mail: alex@genet.sickkids.on.ca