[Genquire-dev] Re: [Genquire-users] Trying to understand somecode

[Mark Wilkinson]

:-(

nope.

There are actually several problems that I can see... but they are easily
fixed, and I am in the middle of coding-up some things that will hopefully
prevent this from happening again.

problems:
    (1) "Gene" should be capitalized
    (2) there should be a feature type called "Transcript"
    (3) both Gene and Transcript should be containers ('Y' instead of 'N')

This will get the Genquire interface to work properly, as these feature
types are hard-coded into the Genquire Adaptor-layer to respond in a
particular way.

Dave, can you spot any other problems?  Are you  going to hard-code the
required feature types in the database schema itself?   That is probably
best... I'll also make a note of this in the documentation.  Danny, you
also had a problem at the beginning with the organism table, right?  That
also needs to be initialized in some way, and noted in the setup docs...

>>sigh<<  it never ends!  :-)

M



Danny Yoo wrote:

> On Tue, 15 Jan 2002, David Block wrote:
>
> > Good point, Mark!
> >
> > I doubt the FeatureType table is populated, but it could be by editing
> > of the "schema" file in the Admin directory.
>
> Here's what's in my FeatureType table now:
>
> mysql> select count(*) from FeatureType;
> +----------+
> | count(*) |
> +----------+
> |        5 |
> +----------+
> 1 row in set (0.02 sec)
>
> mysql> select * from FeatureType;
> +----+----------+-----------+
> | id | type     | container |
> +----+----------+-----------+
> |  1 | Intr     | N         |
> |  2 | gene     | N         |
> |  3 | UTR      | N         |
> |  4 | Repeat   | N         |
> |  5 | RNA Exon | N         |
> +----+----------+-----------+
> 5 rows in set (0.01 sec)
>
> Does this look right to you guys?

--
--------------------------------
"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada