Hi all,
Thanks to the useful advice given by various people, I'm now somewhat
further along in solving my problem but I've hit a problem which I'm not
sure how to resolve. As a bit of background if it helps explain things,
I'm trying to generate marts for multi-species ensembl databases based
on the species_id in coord_system.
I can create a dataset around the table I'm interested in and then use
it as a partition table on the dataset (just a single dataset right
now), but when I run the SQL that's produced, I get a problem which I
suspect is due to me not quite partitioning the table correctly and
trying to select xref types that aren't present in all partitions:
$ mysql -ueg -peg multi_bacterial_mart_51 < msm_part_subdiv.sql
ERROR 1054 (42S22) at line 1207: Unknown column 'a.ox_GO_bool' in 'field
list'
which comes from a create table statement:
create table multi_bacterial_mart_51.TEMP400 as select
a.ox_RefSeqDNA_bool,a.ox_GO_bool,a.ox_integr8_gene_type_1_bool,a.db_display_name_1018,a.\
display_label_1074,a.analysis_id_1020,a.description_1020,a.status_1020,a.seq_region_strand_1020,a.seq_region_id_1020,a.length_1059,a.coord_syst\
em_id_1059,a.ox_EMBLDNA_bool,a.ox_integr8_name_1_bool,a.description_106,a.biotype_1020,a.gene_id_1020_key,a.ox_BioCyc_bool,a.ox_BioCyc_1_bool,a\
.name_106,a.ox_Rfamncrna_bool,a.name_1059,a.species_id_107,a.code_106,a.seq_region_end_1020,a.band_1027,a.attrib_type_id_1060,a.value_1060,a.se\
q_region_start_1020,a.transcript_count,a.is_current_1020,a.display_xref_id_1020,a.value_1022,a.ox_integr8_gene_type_bool,a.ox_ENTREZGENE_bool,a\
.ox_GeneID_bool,a.stable_id_1023,a.ox_GeneID_1_bool,a.ox_integr8_name_bool,a.ox_GO_1_bool,a.source_1020
from multi_bacterial_mart_51.pyrococcus\
_gene_ensembl_37__gene__main as a;
I've tried to use _SUBDIVISION_BOUNDARY_ as suggested in the manual
(although to be honest I'm not sure if I need it!), but this doesn't
seem to have any effect on the SQL produced and doesn't seem to be saved
by martbuilder either in the interface or in the XML file:
<datasetPartitionTable name="coord_system"
selectedColumns="species_id_107">
<partitionApplication name="gene_ensembl"
pCols="species_id_107" dsCols="1.7.0.species_id" relationIds="1955"
nameCols="species\
_id_107" compounds="0"/>
</datasetPartitionTable>
If anyone has any advice on what I might be doing wrong, or how I can
debug this further, I'd appreciate it.
Many thanks,
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]
