Re: Re: [Gusdev-gusdev] SEQ_BROWSER_FEATS

[John I. <io...@pc...>]

Ed,

Here are some statistics about what's in there:

15:47:35 SQL> select count(*) from plasmodb_41.seq_browser_feats;

  COUNT(*)
----------
    219813

Elapsed: 00:00:00.98
15:47:55 SQL> select seq_taxon_name, count(*) from
plasmodb_41.seq_browser_feats group by seq_taxon_name;

SEQ_TAXON_NAME                   COUNT(*)
------------------------------ ----------
Plasmodium falciparum              183502
Plasmodium vivax                    20339
Plasmodium yoelii                   15972

Elapsed: 00:00:00.39
15:48:12 SQL> select count(distinct feat_source_id) from
plasmodb_41.seq_browser_feats;

COUNT(DISTINCTFEAT_SOURCE_ID)
-----------------------------
                        38005

Elapsed: 00:00:07.15

It isn't a materialized view, so it must have been populated by some
script(s).  I'll look around to see if I can find it; it should probably
be re-run anyway.

Meanwhile, I'll see about getting you an export of the data.

John


On Tue, 2004-09-14 at 15:37, Ed Robinson wrote:
> Thanks for the quick reply.  We have a copy of the empty table.  What we need is information on what goes in it and how is it being used?  It is not referenced anywhere else in the modules so we can't make heads or tails of what to put there to make the modules return correctly.
> 
> In the long run, this is not a big deal.  We are anxiously awaiting the new Struts WDK so all of this work will go away shortly.  But we want to have as good looking a T cruzi site as possible in the meantime.
> 
> Thanks!
> -Ed
> 
> 
> 
> > 
> > From: John Iodice <io...@pc...>
> > Date: 2004/09/14 Tue PM 03:27:12 EDT
> > To: Ed Robinson <ed_...@be...>
> > CC: gus...@li...
> > Subject: Re: [Gusdev-gusdev] SEQ_BROWSER_FEATS
> > 
> > Ed,
> > 
> > SEQ_BROWSER_FEATS is a table in the PLASMODB_41 schema of our database. 
> > Here's a description:
> > SQL> desc plasmodb_41.seq_browser_feats
> > Name                                      Null?    Type
> > ----------------------------------------- --------
> > ----------------------------
> > SEQ_TAXON_NAME                            NOT NULL VARCHAR2(30)
> > SEQ_SOURCE_ID                             NOT NULL VARCHAR2(30)
> > START_MIN                                 NOT NULL NUMBER(12)
> > END_MAX                                   NOT NULL NUMBER(12)
> > STRAND                                             VARCHAR2(1)
> > FEAT_TABLE_NAME                           NOT NULL VARCHAR2(30)
> > FEAT_ROW_ID                               NOT NULL NUMBER(12)
> > FEAT_SOURCE_ID                                     VARCHAR2(50)
> > FEAT_PREDICTION_ALGORITHM                          VARCHAR2(50)
> > SPAN_ORDER_NUM                            NOT NULL NUMBER(12)
> > 
> > I think your guess that it's a materialized view is likely correct.  If
> > so, it's likely overdue for refreshing.
> > 
> > John
> > 
> > On Tue, 2004-09-14 at 14:22, Ed Robinson wrote:
> > > We are trying to get parts of the WDK classic up for a release this week, and I am tryning to get the view-contig tool working.  Everything seems good, until you get all the way down into GUSGenomicSequenceTransducer.
> > > 
> > > Suddenly, we are calling on a table named SEQ_BROWSER_FEATS, and try as we might, we just can't comment this sub out.
> > > 
> > > Does anyone know what SEQ_BROWSE_FEATS is?  Is it a temporary table I can make on the fly or is it storing a set of browser display colors?  Any help would be much appreciated.
> > > 
> > > -ed
> > > 
> > > 
> > > Ed Robinson
> > > 255 Deerfield Rd
> > > Bogart, GA 30622
> > > (706)425-9181
> > > http://www.electedrobinson.com
> > > 
> > > --Learn more about the face of your neighbor, and less about your own.
> > >          -Sargent Shriver
> > > 
> > > 
> > > 
> > > 
> > > 
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> > 
> 
> Ed Robinson
> 255 Deerfield Rd
> Bogart, GA 30622
> (706)425-9181
> http://www.electedrobinson.com
> 
> --Learn more about the face of your neighbor, and less about your own.
>          -Sargent Shriver
> 
> 
> 
> 
> 
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