[Bioperl-l] reading and writing GFF3

Scott Cain cain at cshl.edu
Fri Jun 16 23:56:44 EDT 2006


Rob,

I came to the same conclusion as well; I wrote my response as I was
heading out the door and while I was running errands, I realized the
right thing to do is to write a Bio::SeqFeature::Annotated method called
new_from_object, whose usage would be:

  my $my_BSFA = Bio::SeqFeature::Annotated->new_from_object($my_BSFI, %args);

where you would give it a Bio::SeqFeatureI compliant object and try to
create a BSFA like use suggested below.  You could allow passing in args
to control how different things are handled, like mapping non-SO types
to SO types.  I'll think about this over the weekend and let you know if
brilliance strikes me.

Scott


On Fri, 2006-06-16 at 13:31 -0700, Robert Buels wrote:
> Rather than cobble together some ad-hoc solution, I would be interested 
> in working on a good solution to this problem, because it seems like 
> it's just going to get more common as more people start wanting to write 
> GFF3.  What about some code in whatever customarily makes these objects 
> (probably BSF::Annotated's new() method?) that could take another type 
> of Feature object and attempt to shoehorn its data into a new 
> BSF::Annotated?  If it failed (because the type isn't in SO or 
> whatever), it could throw() some informative error message.
> 
> Then, people could write straightforward code something like:
> 
> while(my $oldstylefeature = $features_in->next_feature) {
>     $oldstylefeature->primary_tag('something_that_is_in_so');
>     $oldstylefeature->something_else('some other something that needs to 
> be changed for compliance');
>     my $newfeature = Bio::SeqFeature::Annotated->new($oldstylefeature);
>     $gff3_out->write_feature($newfeature);
> }
> 
> Does that sound like a good idea?  I'd be more than willing to implement 
> this, since I'm going to need to do this sort of thing with many more 
> things than just RepeatMasker.
> 
> Rob
> 
> Scott Cain wrote:
> > 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=
> >>>>> ------------------------------------------------------------------------
> >>>>>
> >>>>> _______________________________________________
> >>>>> Bioperl-l mailing list
> >>>>> Bioperl-l at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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