Hi folks,
Just a quick mail to ask if anyone has any advice for me on how to go
about debugging a problem I have with building marts using MartBuilder.
Without going into huge detail, my problem is with adding data from a
compara schema to my (working) martbuilder definition for our
multi-species ensembl51 schema.
I can successfully build a mart using one partition from my ensembl
schema and its corresponding compara schema, but SQL commands to create
the gene__homology__dm table are never generated. This appears to be
something do with the partitioning of homology, since I get SQL to build
gene__homology__dm generated when partitioning is turned off. Inspection
of the gene_stable_id and member/homology/member_homology table suggests
that there are homologs that can be included by joins betweem the
schema, but this data doesn't appear to be included.
For reference, the partitioning config (inherited from the original
ensembl50.xml file) is:
<datasetPartitionTable name="method_link_species_set"
selectedColumns="method_link_species_set_id_4019_key,name_4010">
<partitionRegex name="name_4010" match="(.).* (...).*"
replace="$1$2"/>
<partitionApplication name="gene_ensembl"
dimension="gene__member" pCols="method_link_species_set_id_4019_key"
dsCols="4.19.0.method_link_species_set_id" nameCols="name_4010"
compounds="0"/>
</datasetPartitionTable>
Interestingly, it seems to refer to the dimension table gene__member
which I can't find in the martbuilder interface, but this might just be
me missing something...
Does anyone have any advice on how I can tackle this problem? For
instance, is there anywhere in martbuilder (even in source) that I can
go to see whats happening behind the scenes?
Many thanks for any help that anyone can offer!
Dan.
--
Dan Staines, PhD
EMBL-European Bioinformatics Institute Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus, Hinxton Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK email: [EMAIL PROTECTED]
