Chromosomes strike again

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Chromosomes strike again

Vallejos, Andrew

Caused by: java.lang.RuntimeException: IllegalAccessException while trying to get value of field "chromosome" in object: Gene [chromosome=629000008, chromosomeLocation=630035768,

description="protein tyrosine phosphatase involved in regulation of mitogen-activated protein kinase (MAPK)", downstreamIntergenicRegion=null, ensemblIdentifier="null", fishBand

="q13", geneType="protein-coding", id="629026857", length="4231", name="dual specificity phosphatase 6", ncbiGeneNumber="116663", nomenclatureStatus="APPROVED", organism=62900000

0, pharmGKBidentifier="PA27529", primaryIdentifier="70978", score="null", scoreType="null", secondaryIdentifier="RGD:70978", sequence=null, sequenceOntologyTerm=630000004, symbol

="Dusp6", upstreamIntergenicRegion=null]

 

So it seems like I have not quite worked out all the chromosome bugs.

 

-Andrew

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]


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Re: Chromosomes strike again

Vallejos, Andrew

production-rat=# select c.id, c.primaryidentifier, count(g.id) from chromosome as c, gene as g where c.id = g.chromosomeid group by c.id, c.primaryidentifier;

    id     | primaryidentifier | count

-----------+-------------------+-------

629000019 | 18                |   505

629000005 | 4                 |  1283

629000017 | 16                |   578

629000016 | 15                |   706

629000014 | 13                |   613

629000004 | 3                 |  1662

629000018 | 17                |   648

629000010 | 9                 |   751

629000003 | 2                 |  1346

629000023 | X                 |   822

629000002 | 1                 |  2821

(11 rows)

 

Looks like only some of the genes have valid chromosomes. 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Vallejos, Andrew
Sent: Wednesday, December 01, 2010 12:52 PM
To: Intermine
Subject: [InterMine Dev] Chromosomes strike again

 

Caused by: java.lang.RuntimeException: IllegalAccessException while trying to get value of field "chromosome" in object: Gene [chromosome=629000008, chromosomeLocation=630035768,

description="protein tyrosine phosphatase involved in regulation of mitogen-activated protein kinase (MAPK)", downstreamIntergenicRegion=null, ensemblIdentifier="null", fishBand

="q13", geneType="protein-coding", id="629026857", length="4231", name="dual specificity phosphatase 6", ncbiGeneNumber="116663", nomenclatureStatus="APPROVED", organism=62900000

0, pharmGKBidentifier="PA27529", primaryIdentifier="70978", score="null", scoreType="null", secondaryIdentifier="RGD:70978", sequence=null, sequenceOntologyTerm=630000004, symbol

="Dusp6", upstreamIntergenicRegion=null]

 

So it seems like I have not quite worked out all the chromosome bugs.

 

-Andrew

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]


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