[Bioperl-l] bp_genbank2gff3.pl - circular genomes, origin-spanning features, and GFF3

[Chris Fields]

On Apr 10, 2010, at 11:23 AM, Leighton Pritchard wrote:

> Hi Nathan, 
> 
> Thanks for checking this out.  The problem's actually with NC_002128.gbk -
> there's a typo in my email to the list; NC_002127.gbk is good on my system
> (I was swapping between 2128 and 2127 to try to see what could be going
> wrong; sending a draft by accident probably didn't help either ;) ).  Sorry
> about that.
> 
> I'm cc-ing this back to the list so that the error is noted in the archive
> (and to announce to the world that I can't type straight ;))
> 
> On 09/04/2010 Friday, April 9, 21:06, "Nathan Liles" <nml5566 at gmail.com>
> wrote:
> 
>> The converter has been patched to handle merged circular genomes, but
>> there was an unexpected problem, so I had to comment it out. I may
>> enable it as an optional feature in the future.
> 
> That sounds like a useful feature to have, when it's fixed.  We've quite a
> few bacterial genomes to deal with, so it will get some use.
> 
> Cheers,
> 
> L.

Leighton, Nathan,

I'm planning doing a fairly large-scale project this summer involving Bio::DB::SF::Store, the SQLite, adaptor, and bacterial genomes that will require things to work correctly (i.e. features that cross the origin to be joined in the right order, etc etc).  So, if there is anything borked I'll definitely be pushing for a fix.

chris