[Bioperl-l] reading and writing GFF3

Scott Cain cain at cshl.edu
Fri Jun 16 15:55:31 EDT 2006


Um, yeah, good question.  The reason I didn't answer you when you wrote
before is that I was hoping for divine inspiration for an answer (or for
somebody else to answer, which would have been really great :-)

The short answer (and easy one for me to type) is that you will probably
need an ad hoc method to do it, which is the same thing I do when I need
to convert gff2 to gff3, to make sure the things I need mapped get
mapped the 'right' way (that is, the way I want them to go).  I don't
have any sample code that does this, but if you want to start working up
an ad hoc method, I will certainly try to help you as much as I can.

Scott


On Fri, 2006-06-16 at 12:34 -0700, Robert Buels wrote:
> So about that converting ye olde feature objects into 
> Bio::SeqFeature::Annotated objects.  How do I do it?
> 
> 
> Scott Cain wrote:
> > That's OK--You added a few items that should be escaped that weren't, so
> > I added those too.
> >
> > Thanks,
> > Scott
> >
> >
> > On Fri, 2006-06-16 at 12:30 -0700, Robert Buels wrote:
> >   
> >> Woops, I should have said something about that.  I submitted it before
> >> I saw that Scott had already done the escaping in CVS.
> >>
> >> Chris Fields wrote: 
> >>     
> >>> Scott, 
> >>>
> >>> Looks like Robert also submitted a bug report related to this as well


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