[Bioperl-l] genbank2gff and how do I use gff3 with Bio::DB::GFF?

Scott Cain cain at cshl.edu
Tue Jun 14 16:53:29 EDT 2005

Hi Chad,

Sorry I haven't reproduced your results; I've been dragged down by other
matters.  If I can recap to make sure I have it right:

 bp_genbank2gff.pl will correctly generate gff2
 bp_genbank2gff3.pl will correctly generate gff3

If I have that right, I would be reluctant to pitch bp_genbank2gff.pl as
there are still plenty of people (that is, the overwhelming majority)
that use gff2.  I nearly certain (without even looking) that they could
be documented better.

What would be really great would be if you could submit this as a bug on
bioperl's bugzilla, so I won't forget about it.  I have a few software
releases I really want to get out in the next week or so, so I know I
won't get to it real soon.


On Tue, 2005-06-14 at 11:02 -0600, Chad Matsalla wrote:
> Greetings,
> It's a bit cheesy to follow up on my own post but due to the
> underwhelming response I thought I'd tell people that evertything works
> fine if you use bp_genbank2gff3.pl.
> Since bp_genbank2gff.pl doesn't work quite properly and hasn't been
> changed for over a year can it just be moved to the attic to prevent
> other people from trying[1] to work with it?
> Thanks!
> Chad Matsalla
> [1] For some strange reason.
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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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