On 12 Aug 2006, at 09:49, Arek Kasprzyk wrote:
I'm still working on getting a sequence mart attached to data that
I've
been dumping out of a Chado database. I've been using the Ensembl
datasets as an example, and I've got a working feature database and
(structurally, at least) a clone of the Ensembl sequence_mart
database.
I can't seem to figure out how to connect them; part of this is
because
when I connect to the ensembl_mart database using MartExplorer, I
don't
see where I can get to the same sequence data dataset that's visible
on
the MartView page via Ensembl. Am I missing some sort of local
configuration files that aren't pulled in with a database import? How
do
I actually tell the tools that I want to connect a feature dataset and
sequence dataset?
Hi,
I am not sure if you can reproduce this functionality
with MExplorer. MartJ query library is quite dated and it is missing
quite a bit of functionality which is now part of perl code base
(MartView),
so it is quite possible that ensembl sequence mart awareness is
hardcoded
to some extent in MartJ.
We can happily guide you through the connection logic using MView if
you
want. Is MExplorer sequence essential or are you happy to switch to
MView instead?
For MView you simply specify appropriate importables and exportables
on your feature and sequence datasets. (you will also need a structure
datataset)
For examples look at ensembl mart tables and appropriate dataset
configuration
using MEditor
it has just occurred to me, maybe the problem is simpler that it seems.
Have you configured your marts with MEditor? Could you also send
us your registry file that you are using?
cheers,
a.
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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