SpanUpload /Regions Tab

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

SpanUpload /Regions Tab

kkarra@stanford.edu
Hi,

SpanUpload doesn't seem to be working for me..

Check this template

http://yeastgenome-yeastmine-test.stanford.edu:8080/yeastmine-dev/template.do?name=ChromosomeRegion_AllGenes

I get 8 ORFs on chr14:1..20000

If I use Regions Tab and select 'ORF' in the list of Feature Type and enter chr14:1..20000, I don't get any results back..there are no errors in intermine.log, here is the SQL it runs..


18/07/11,13:19:50 INFO                              sqllogger     - (VERBOSE) iql: SELECT DISTINCT a9_.id AS a1_, a9_.primaryIdentifier AS a2_, a9_.class AS a3_, a7_.primaryIdentifier AS a4_, a10_.start AS a5_, a10_.end AS a6_ FROM org.intermine.model.bio.Chromosome AS a7_, org.intermine.model.bio.Organism AS a8_, org.intermine.model.bio.SequenceFeature AS a9_, org.intermine.model.bio.Location AS a10_ WHERE (a9_.organism CONTAINS a8_ AND a8_.shortName = 'S. cerevisiae' AND a10_.feature CONTAINS a9_ AND a10_.locatedOn CONTAINS a7_ AND a7_.primaryIdentifier = '14' AND a9_.class IN ? AND RANGE(1, 20000, a10_.locatedOn) OVERLAPS RANGE(a10_.start, a10_.end, a10_.locatedOn)) ORDER BY a10_.start 1: [interface org.intermine.model.bio.ORF]

generated sql: SELECT DISTINCT a9_.id AS a1_, a9_.primaryIdentifier AS a2_, a9_.class AS a3_, a7_.primaryIdentifier AS a4_, a10_.intermine_start AS a5_, a10_.intermine_end AS a6_ FROM Chromosome AS a7_, Organism AS a8_, SequenceFeature AS a9_, Location AS a10_ WHERE a9_.organismId = a8_.id AND a8_.shortName = 'S. cerevisiae' AND a10_.featureId = a9_.id AND a10_.locatedOnId = a7_.id AND a7_.primaryIdentifier = '14' AND a9_.class IN ('org.intermine.model.bio.ORF') AND a10_.locatedOnId = a10_.locatedOnId AND bioseg_create(1, 20000) && bioseg_create(a10_.intermine_start, a10_.intermine_end) ORDER BY a10_.intermine_start, a9_.id, a7_.primaryIdentifier, a10_.intermine_end LIMIT 1000


optimised sql: SELECT DISTINCT a9_.id AS a1_, a9_.primaryIdentifier AS a2_, a9_.class AS a3_, a7_.primaryIdentifier AS a4_, a10_.intermine_start AS a5_, a10_.intermine_end AS a6_ FROM Chromosome AS a7_, Organism AS a8_, SequenceFeature AS a9_, Location AS a10_ WHERE a9_.organismId = a8_.id AND a8_.shortName = 'S. cerevisiae' AND a10_.featureId = a9_.id AND a10_.locatedOnId = a7_.id AND a7_.primaryIdentifier = '14' AND a9_.class IN ('org.intermine.model.bio.ORF') AND a10_.locatedOnId = a10_.locatedOnId AND bioseg_create(1, 20000) && bioseg_create(a10_.intermine_start, a10_.intermine_end) ORDER BY a10_.intermine_start, a9_.id, a7_.primaryIdentifier, a10_.intermine_end LIMIT 1000

bag tables: 0 ms, generate: 0 ms, optimise: 0 ms,  ms,  estimate: 3 ms, execute: 3 ms, convert results: 0 ms, extra queries: 0 ms, total: 6 ms, rows: 0

Not sure why 14 instead of chr14 is used as the primaryIdentifier in SQL..

What am I doing wrong?

Thanks,
-Kalpana




_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: SpanUpload /Regions Tab

Richard Smith
Hi Kalpana,
You're not doing anything wrong, this is a bug with the region upload.

In the Mines we maintain we don't prefix chromosome identifiers with
chr.  It looks like the code strips this off, assuming it is an artifact
of uploading BED format.  We'll release a fix soon.

Richard.



On 18/07/2011 21:22, Kalpana Karra wrote:

> Hi,
>
> SpanUpload doesn't seem to be working for me..
>
> Check this template
>
> http://yeastgenome-yeastmine-test.stanford.edu:8080/yeastmine-dev/template.do?name=ChromosomeRegion_AllGenes
>
> I get 8 ORFs on chr14:1..20000
>
> If I use Regions Tab and select 'ORF' in the list of Feature Type and enter chr14:1..20000, I don't get any results back..there are no errors in intermine.log, here is the SQL it runs..
>
>
> 18/07/11,13:19:50 INFO                              sqllogger     - (VERBOSE) iql: SELECT DISTINCT a9_.id AS a1_, a9_.primaryIdentifier AS a2_, a9_.class AS a3_, a7_.primaryIdentifier AS a4_, a10_.start AS a5_, a10_.end AS a6_ FROM org.intermine.model.bio.Chromosome AS a7_, org.intermine.model.bio.Organism AS a8_, org.intermine.model.bio.SequenceFeature AS a9_, org.intermine.model.bio.Location AS a10_ WHERE (a9_.organism CONTAINS a8_ AND a8_.shortName = 'S. cerevisiae' AND a10_.feature CONTAINS a9_ AND a10_.locatedOn CONTAINS a7_ AND a7_.primaryIdentifier = '14' AND a9_.class IN ? AND RANGE(1, 20000, a10_.locatedOn) OVERLAPS RANGE(a10_.start, a10_.end, a10_.locatedOn)) ORDER BY a10_.start 1: [interface org.intermine.model.bio.ORF]
>
> generated sql: SELECT DISTINCT a9_.id AS a1_, a9_.primaryIdentifier AS a2_, a9_.class AS a3_, a7_.primaryIdentifier AS a4_, a10_.intermine_start AS a5_, a10_.intermine_end AS a6_ FROM Chromosome AS a7_, Organism AS a8_, SequenceFeature AS a9_, Location AS a10_ WHERE a9_.organismId = a8_.id AND a8_.shortName = 'S. cerevisiae' AND a10_.featureId = a9_.id AND a10_.locatedOnId = a7_.id AND a7_.primaryIdentifier = '14' AND a9_.class IN ('org.intermine.model.bio.ORF') AND a10_.locatedOnId = a10_.locatedOnId AND bioseg_create(1, 20000)&&  bioseg_create(a10_.intermine_start, a10_.intermine_end) ORDER BY a10_.intermine_start, a9_.id, a7_.primaryIdentifier, a10_.intermine_end LIMIT 1000
>
>
> optimised sql: SELECT DISTINCT a9_.id AS a1_, a9_.primaryIdentifier AS a2_, a9_.class AS a3_, a7_.primaryIdentifier AS a4_, a10_.intermine_start AS a5_, a10_.intermine_end AS a6_ FROM Chromosome AS a7_, Organism AS a8_, SequenceFeature AS a9_, Location AS a10_ WHERE a9_.organismId = a8_.id AND a8_.shortName = 'S. cerevisiae' AND a10_.featureId = a9_.id AND a10_.locatedOnId = a7_.id AND a7_.primaryIdentifier = '14' AND a9_.class IN ('org.intermine.model.bio.ORF') AND a10_.locatedOnId = a10_.locatedOnId AND bioseg_create(1, 20000)&&  bioseg_create(a10_.intermine_start, a10_.intermine_end) ORDER BY a10_.intermine_start, a9_.id, a7_.primaryIdentifier, a10_.intermine_end LIMIT 1000
>
> bag tables: 0 ms, generate: 0 ms, optimise: 0 ms,  ms,  estimate: 3 ms, execute: 3 ms, convert results: 0 ms, extra queries: 0 ms, total: 6 ms, rows: 0
>
> Not sure why 14 instead of chr14 is used as the primaryIdentifier in SQL..
>
> What am I doing wrong?
>
> Thanks,
> -Kalpana
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev