[Bioperl-l] Re: genbank chado loader or gff3 producer

[Lincoln Stein]

In that case, the load_genbank.pl script (which is my modification of your 
load_embl.pl script) has a -stdout option, which conveniently enough, 
produces GFF3 format output.

Lincoln

On Thursday 17 July 2003 11:48 am, Scott Cain wrote:
> Lincoln,
>
> I don't think so (though I hope Chris will correct me if I am wrong); it
> his docs for Bio::SeqFeature::Tools::Unflattener, he indicates that it
> should now be easier to create a GenBank to GFF3 converter, but I don't
> think he actually created one.
>
> Scott
>
> On Thu, 2003-07-17 at 11:25, Lincoln Stein wrote:
> > Hi Scott,
> >
> > Chris Mungall just contributed a genbank to gff3 converter to Bioperl,
> > although I'm having trouble finding it in the repository right now.
> >
> > Lincoln
> >
> > On Wednesday 16 July 2003 04:14 pm, Scott Cain wrote:
> > > Lincoln,
> > >
> > > As I was thinking about creating a genbank file loader for chado, it
> > > occurred to me that it might be better to make a more general genbank
> > > to gff3 converter, then make a gff3 loader for chado (a tool that I
> > > have been planning on writing as well).  Does that sound reasonable to
> > > you?
> > >
> > > Scott

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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