[BioSQL-l] SeqFeature scores

[Mark Johnson]

On Tue, Oct 14, 2008 at 12:28 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Oct 14, 2008, at 11:03 AM, Mark Johnson wrote:
>
>> On Mon, Oct 13, 2008 at 3:03 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
>>>
>>> Hi Mark, this was a known bug at some point. In fact, I can't swear that
>>> it
>>> was solved, so if you are running the latest bioperl-db version then I
>>> think
>>> it hasn't been. Can you confirm?
>>>
>>>      -hilmar
>>
>> I just pointed my scriptage to a freshly updated bioperl-live and
>> bioperl-db (updated via svn a few minutes ago).  I'm seeing the same
>> problem.  So, unless I'm hallucinating, this is still an issue.  Shall
>> I open a new bug in bugzilla, or is there an old one you'd like to
>> reopen?
>
> I think open a new bug so we can track it.  Personally I'm not sure how we'd
> store score data in BioSQL.  Is 'score' within the schema?  I suppose we
> could add it as a specific tag value but that seems potentially hackish and
> prone to naming conflicts.
>
> chris

Well, if there is no provision for storing score in the schema, it's
not a bug, it's an enhancement request.  If it worked in the past or
is supposed to work, it's a bug.  As to where it ends up in the
schema, I had been wondering about that.  I presumed it ended up with
the rest of the tags...and I wonder if that's not the most appropriate
place for it.  It's an attribute that not all features have.  In fact,
I don't see score as part of SeqFeatureI.  Bio::SeqFeature::Generic
has it's own accessor and storage.  Speaking of which, I just tried to
go browsing the deobfuscator and it seems to be horked (internal
server error). Is there a better contact other than dag at sonsorol.org
(server administrator)?   Is there a bugzilla queue for website
issues?