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.
> > >
> > >
> > >
>
____________________________________________________________________________________
> > > Never miss a thing. Make Yahoo your home page.
> > > http://www.yahoo.com/r/hs
> > >
> > >
> > >
>
-------------------------------------------------------------------------
> > > This SF.net email is sponsored by: Microsoft
> > > Defy all challenges. Microsoft(R) Visual Studio
> 2008.
> > >
>
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > > _______________________________________________
> > > Gmod-gbrowse mailing list
> > > [email protected]
> > >
>
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >
> >
> >
> >
> --
>
------------------------------------------------------------------------
> 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
-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
Gmod-gbrowse mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
