[ensembl-dev] querying a copy of the ensembl human variation 72_37

Jayaraman, Pushkala pjayaraman at mcw.edu
Thu Sep 5 20:38:41 BST 2013


Heres my query:

select
vf.variation_name, vf.seq_region_id, vf.seq_region_start, vf.source_id,
s.name, vf.minor_allele_freq, tv.feature_stable_id, tv.allele_string, tv.consequence_types
from
variation_feature vf,
transcript_variation tv,
source s
WHERE
s.source_id=vf.source_id and
vf.variation_feature_id=tv.variation_feature_id and
--tv.feature_stable_id ='ENST00000544455'
tv.feature_stable_id in
('ENST00000380152','ENST00000530893','ENST00000528762','ENST00000470094','ENST00000533776','ENST00000544455')
and
vf.variation_id not in
(
select
vf.variation_id
from
variation_feature vf,
transcript_variation tv,
failed_variation fv
where
fv.variation_id=vf.variation_id
and
vf.variation_feature_id=tv.variation_feature_id
and
--tv.feature_stable_id ='ENST00000544455'
tv.feature_stable_id in
('ENST00000380152','ENST00000530893','ENST00000528762','ENST00000470094','ENST00000533776','ENST00000544455')
)



When I try this on my local copy.. it runs for 5 mins with no result!

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Jayaraman, Pushkala
Sent: Thursday, September 05, 2013 2:25 PM
To: dev at ensembl.org
Subject: [ensembl-dev] querying a copy of the ensembl human variation 72_37

Hello,
I seem to be having trouble querying the failed_variation table
I cannot even seem to get count of the rows..
Is there any additional indexes you guys apply to the failed_variation table?

Pushkala Jayaraman
Programmer/Analyst - Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
414-955-2229
http://rgd.mcw.edu

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