Hi Mustafa,
This is not a bug, rather it is normal behavior for a GFF3 database.
Aggregators are not used when data are loaded in a GFF3 database with
Bio::DB::SeqFeature::Store, as multilevel features are supposed to
have their structure encoded in the GFF3 itself.
I'm not sure if it will work with your GFF, but what happens if you
set the feature=bin? Or try changing the "ID=" to "Parent=" on the
bin feaures and creating one full length cds_density feature for each
chromosome that has the ID=NC_004347:CDS (for example).
Sheldon
On Fri, Feb 15, 2008 at 9:30 AM, Syed Mustafa Hussain
<[EMAIL PROTECTED]> wrote:
> Hi Scott,
>
> I still have problem with histogram plot. Please let
> me know what additional information might help us
> solve this problem. Below you will find relevant code
> and data. It worked fine with in-memory GFF files, but
> no plot is drawn when I loaded this in MySQL using
> bp_seqfeature_load.PLS.
>
> db_adaptor = Bio::DB::SeqFeature::Store
> db_args = -adaptor DBI::mysql
> -dsn dbi:mysql:xxx
> -user xxx
> -password xxx
>
>
> cds_density{bin:CDS}
>
> [cds_density:overview]
> feature = cds_density
> glyph = xyplot
> graph_type = boxes
> scale = right
> bgcolor = black
> fgcolor = black
> height = 20
> key = cds density
>
> NC_004347 CDS bin 1270000 1280000 7
> + . ID=NC_004347:CDS;Name=NC_004347:CDS
> NC_004347 CDS bin 320000 330000 9
> + . ID=NC_004347:CDS;Name=NC_004347:CDS
> NC_004347 CDS bin 900000 910000 11
> + . ID=NC_004347:CDS;Name=NC_004347:CDS
> NC_004347 CDS bin 2760000 2770000 10
> + . ID=NC_004347:CDS;Name=NC_004347:CDS
> NC_004347 CDS bin 4430000 4440000 11
> + . ID=NC_004347:CDS;Name=NC_004347:CDS
> NC_004347 CDS bin 710000 720000 9
> + . ID=NC_004347:CDS;Name=NC_004347:CDS
>
> Regards,
> Mustafa Syed.
> --- Scott Cain <[EMAIL PROTECTED]> wrote:
>
> > Hi Mustafa,
> >
> > I am curious if Sheldon's suggestion fixed your
> > problem. It doesn't
> > feel to me like it should be necessary, assuming you
> > have a reference
> > sequence line for your features in GFF, like this:
> >
> > NC_009999 . region 1 1000000 . . .
> > ID=NC_009999
> >
> > However, I'm currently trying to debug behavior like
> > this right now, so
> > any information you could provide would be
> > appreciated.
> >
> > Thanks,
> > Scott
> >
> > On Mon, 2008-02-11 at 13:21 -0500, Sheldon McKay
> > wrote:
> > > Hi Mustafa,
> > >
> > > When I encounter this problem, I usually try
> > adding a sequence-region
> > > directive for each reference sequence (with the
> > absolute start and end
> > > coordinates), so that a full-length feature of
> > that name and length
> > > will be autogenerated when the GFF is processed
> > for database loading.
> > >
> > > ##sequence-region NC_009999 1 1000000
> > >
> > > Sheldon
> > >
> > > On Feb 11, 2008 12:31 PM, Syed Mustafa Hussain
> > <[EMAIL PROTECTED]> wrote:
> > > > Hi,
> > > >
> > > > I recently switched from in-memory to MySQL and
> > have
> > > > used bp_seqfeature_load.PLS script to create
> > and load
> > > > MySQL tables.
> > > >
> > > > Gbrowse interface is giving me the following
> > error:
> > > >
> > > > "The landmark named NC_004347:3359971..3369971
> > is not
> > > > recognized. See the help pages for suggestions"
> > > >
> > > > What might be wrong with database causing this
> > error?
> > > >
> > > > Where can I get schema diagram to understand
> > > > relational database created by above script.
> > > >
> > > > Mustafa.
> > > >
> > > >
> > > >
> >
>
> ____________________________________________________________________________________
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> > > >
> > > >
> > > >
> >
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> >
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> > >
> > >
> > --
> >
> ------------------------------------------------------------------------
> > Scott Cain, Ph. D.
> > [EMAIL PROTECTED]
> > GMOD Coordinator (http://www.gmod.org/)
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> >
> >
>
>
>
>
>
> ____________________________________________________________________________________
> Never miss a thing. Make Yahoo your home page.
> http://www.yahoo.com/r/hs
>
--
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
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Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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