Hi Sheldon,
Thanks! It worked when I used bin:CDS for feature
instead of giving aggregator name. As you explained
GFF3 database is inherent multilevel feature capable
and need no explicit aggregator definition, unlike
in-memory adaptor. It is good to add this note in
tutorial.
Regards,
Mustafa Syed.
----- Sheldon McKay <[EMAIL PROTECTED]> wrote:
> 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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> > > >
> > > >
> > > >
> > > --
> > >
> >
>
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> > > Scott Cain, Ph. D.
>
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