Qtls and Chromosomes

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Qtls and Chromosomes

Vallejos, Andrew

I’ve gone through all my keys, data script, Intermine-xml file, and run a clean-all, and I don’t see anything wrong.

 

I usually get the following results; sometimes I get chromosomes for QTLs but not for genes.

 

production-rat=# select count(*), chromosomeid from gene group by chromosomeid;

 

 

 count | chromosomeid

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

 18856 |            

  1346 |    546000003

   594 |    546000021

   541 |    546000020

   808 |    546000007

   595 |    546000013

  1632 |    546000011

   505 |    546000019

   554 |    546000012

  1183 |    546000009

  1662 |    546000004

   706 |    546000016

   613 |    546000014

   693 |    546000015

   822 |    546000023

  1283 |    546000005

  1274 |    546000006

   751 |    546000010

   578 |    546000017

  2821 |    546000002

  1286 |    546000008

   648 |    546000018

(22 rows)

 

production-rat=# select count(*), chromosomeid from qtl group by chromosomeid;

 count | chromosomeid

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

  1774 |            

(1 row)

 

 

 

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

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


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Re: Qtls and Chromosomes

Julie Sullivan
Hi Andrew,

In the XML you sent the other day, I don't see the gene.chromosome or
QTL.chromosome relationships assigned.

Which source sets those?  Or do you use the "create-chromosome"
post-process to fill those in?

Cheers,
Julie

> I've gone through all my keys, data script, Intermine-xml file, and run
> a clean-all, and I don't see anything wrong.
>
>
>
> I usually get the following results; sometimes I get chromosomes for
> QTLs but not for genes.
>
>
>
> production-rat=# select count(*), chromosomeid from gene group by
> chromosomeid;
>
>
>
>
>
>  count | chromosomeid
>
> -------+--------------
>
>  18856 |
>
>   1346 |    546000003
>
>    594 |    546000021
>
>    541 |    546000020
>
>    808 |    546000007
>
>    595 |    546000013
>
>   1632 |    546000011
>
>    505 |    546000019
>
>    554 |    546000012
>
>   1183 |    546000009
>
>   1662 |    546000004
>
>    706 |    546000016
>
>    613 |    546000014
>
>    693 |    546000015
>
>    822 |    546000023
>
>   1283 |    546000005
>
>   1274 |    546000006
>
>    751 |    546000010
>
>    578 |    546000017
>
>   2821 |    546000002
>
>   1286 |    546000008
>
>    648 |    546000018
>
> (22 rows)
>
>
>
> production-rat=# select count(*), chromosomeid from qtl group by
> chromosomeid;
>
>  count | chromosomeid
>
> -------+--------------
>
>   1774 |
>
> (1 row)
>
>
>
>
>
>
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



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Re: Qtls and Chromosomes

Alex Kalderimis
Ah yes - that is the change I made in the qtl script (switching from
unless to if on the chrom test - at present it will never set
chromosomes).

I haven't sorted out checking in (pushing) yet, due to technical
difficulties, but I shall look at that now.

Alex

On Mon, 2010-11-22 at 17:23 +0000, [hidden email] wrote:

> Hi Andrew,
>
> In the XML you sent the other day, I don't see the gene.chromosome or
> QTL.chromosome relationships assigned.
>
> Which source sets those?  Or do you use the "create-chromosome"
> post-process to fill those in?
>
> Cheers,
> Julie
>
> > I've gone through all my keys, data script, Intermine-xml file, and run
> > a clean-all, and I don't see anything wrong.
> >
> >
> >
> > I usually get the following results; sometimes I get chromosomes for
> > QTLs but not for genes.
> >
> >
> >
> > production-rat=# select count(*), chromosomeid from gene group by
> > chromosomeid;
> >
> >
> >
> >
> >
> >  count | chromosomeid
> >
> > -------+--------------
> >
> >  18856 |
> >
> >   1346 |    546000003
> >
> >    594 |    546000021
> >
> >    541 |    546000020
> >
> >    808 |    546000007
> >
> >    595 |    546000013
> >
> >   1632 |    546000011
> >
> >    505 |    546000019
> >
> >    554 |    546000012
> >
> >   1183 |    546000009
> >
> >   1662 |    546000004
> >
> >    706 |    546000016
> >
> >    613 |    546000014
> >
> >    693 |    546000015
> >
> >    822 |    546000023
> >
> >   1283 |    546000005
> >
> >   1274 |    546000006
> >
> >    751 |    546000010
> >
> >    578 |    546000017
> >
> >   2821 |    546000002
> >
> >   1286 |    546000008
> >
> >    648 |    546000018
> >
> > (22 rows)
> >
> >
> >
> > production-rat=# select count(*), chromosomeid from qtl group by
> > chromosomeid;
> >
> >  count | chromosomeid
> >
> > -------+--------------
> >
> >   1774 |
> >
> > (1 row)
> >
> >
> >
> >
> >
> >
> >
> > ======================
> >
> > Andrew Vallejos
> >
> > Web Developer II
> >
> > Biotechnology and Bioengineering Center
> >
> > Medical College of Wisconsin
> >
> > 414-955-4104
> >
> > [hidden email]
> >
> >
> >
> > _______________________________________________
> > 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



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Re: Qtls and Chromosomes

Vallejos, Andrew
Really?  Because looking at the Intermine.xml file...

   <item id="0_26" class="" implements="QTL">
      <attribute name="symbol" value="Eae5" />
      <attribute name="primaryIdentifier" value="61324" />
      <attribute name="name" value="Experimental allergic
encephalomyelitis QTL 5" />
      <attribute name="lod" value="13.0" />
      <attribute name="trait" value="Brain/spinal cord inflammation" />
      <collection name="publications">
         <reference ref_id="0_25" />
      </collection>
      <reference name="organism" ref_id="0_1" />
   </item>
   <item id="0_27" class="" implements="Location">
      <attribute name="end" value="24470522" />
      <reference name="feature" ref_id="0_26" />
      <reference name="locatedOn" ref_id="0_13" /> <!-- ref to
Chromosome 12 -->
      <attribute name="start" value="20932559" />
   </item>

I have a Location, which references the Chromosome and the QTL.


-----Original Message-----
From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex
Kalderimis
Sent: Monday, November 22, 2010 11:33 AM
To: [hidden email]
Cc: Vallejos, Andrew; Intermine
Subject: Re: [InterMine Dev] Qtls and Chromosomes

Ah yes - that is the change I made in the qtl script (switching from
unless to if on the chrom test - at present it will never set
chromosomes).

I haven't sorted out checking in (pushing) yet, due to technical
difficulties, but I shall look at that now.

Alex

On Mon, 2010-11-22 at 17:23 +0000, [hidden email] wrote:

> Hi Andrew,
>
> In the XML you sent the other day, I don't see the gene.chromosome or
> QTL.chromosome relationships assigned.
>
> Which source sets those?  Or do you use the "create-chromosome"
> post-process to fill those in?
>
> Cheers,
> Julie
>
> > I've gone through all my keys, data script, Intermine-xml file, and
run

> > a clean-all, and I don't see anything wrong.
> >
> >
> >
> > I usually get the following results; sometimes I get chromosomes for
> > QTLs but not for genes.
> >
> >
> >
> > production-rat=# select count(*), chromosomeid from gene group by
> > chromosomeid;
> >
> >
> >
> >
> >
> >  count | chromosomeid
> >
> > -------+--------------
> >
> >  18856 |
> >
> >   1346 |    546000003
> >
> >    594 |    546000021
> >
> >    541 |    546000020
> >
> >    808 |    546000007
> >
> >    595 |    546000013
> >
> >   1632 |    546000011
> >
> >    505 |    546000019
> >
> >    554 |    546000012
> >
> >   1183 |    546000009
> >
> >   1662 |    546000004
> >
> >    706 |    546000016
> >
> >    613 |    546000014
> >
> >    693 |    546000015
> >
> >    822 |    546000023
> >
> >   1283 |    546000005
> >
> >   1274 |    546000006
> >
> >    751 |    546000010
> >
> >    578 |    546000017
> >
> >   2821 |    546000002
> >
> >   1286 |    546000008
> >
> >    648 |    546000018
> >
> > (22 rows)
> >
> >
> >
> > production-rat=# select count(*), chromosomeid from qtl group by
> > chromosomeid;
> >
> >  count | chromosomeid
> >
> > -------+--------------
> >
> >   1774 |
> >
> > (1 row)
> >
> >
> >
> >
> >
> >
> >
> > ======================
> >
> > Andrew Vallejos
> >
> > Web Developer II
> >
> > Biotechnology and Bioengineering Center
> >
> > Medical College of Wisconsin
> >
> > 414-955-4104
> >
> > [hidden email]
> >
> >
> >
> > _______________________________________________
> > 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



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Re: Qtls and Chromosomes

Julie Sullivan
The XML below will populate the QTL.location reference and the
QTL.location.locatedOn (which is a chromosome) reference but not
QTL.chromosome.

In the query below you were looking in the QTL table for chromosome ID.
You don't have that relationship in your XML file so QTL.chromosomeid will
be empty after loading that source.

You can set this in your XML file or use the post-process create-chromosome.

> Really?  Because looking at the Intermine.xml file...
>
>    <item id="0_26" class="" implements="QTL">
>       <attribute name="symbol" value="Eae5" />
>       <attribute name="primaryIdentifier" value="61324" />
>       <attribute name="name" value="Experimental allergic
> encephalomyelitis QTL 5" />
>       <attribute name="lod" value="13.0" />
>       <attribute name="trait" value="Brain/spinal cord inflammation" />
>       <collection name="publications">
>          <reference ref_id="0_25" />
>       </collection>
>       <reference name="organism" ref_id="0_1" />
>    </item>
>    <item id="0_27" class="" implements="Location">
>       <attribute name="end" value="24470522" />
>       <reference name="feature" ref_id="0_26" />
>       <reference name="locatedOn" ref_id="0_13" /> <!-- ref to
> Chromosome 12 -->
>       <attribute name="start" value="20932559" />
>    </item>
>
> I have a Location, which references the Chromosome and the QTL.
>
>
> -----Original Message-----
> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex
> Kalderimis
> Sent: Monday, November 22, 2010 11:33 AM
> To: [hidden email]
> Cc: Vallejos, Andrew; Intermine
> Subject: Re: [InterMine Dev] Qtls and Chromosomes
>
> Ah yes - that is the change I made in the qtl script (switching from
> unless to if on the chrom test - at present it will never set
> chromosomes).
>
> I haven't sorted out checking in (pushing) yet, due to technical
> difficulties, but I shall look at that now.
>
> Alex
>
> On Mon, 2010-11-22 at 17:23 +0000, [hidden email] wrote:
>> Hi Andrew,
>>
>> In the XML you sent the other day, I don't see the gene.chromosome or
>> QTL.chromosome relationships assigned.
>>
>> Which source sets those?  Or do you use the "create-chromosome"
>> post-process to fill those in?
>>
>> Cheers,
>> Julie
>>
>> > I've gone through all my keys, data script, Intermine-xml file, and
> run
>> > a clean-all, and I don't see anything wrong.
>> >
>> >
>> >
>> > I usually get the following results; sometimes I get chromosomes for
>> > QTLs but not for genes.
>> >
>> >
>> >
>> > production-rat=# select count(*), chromosomeid from gene group by
>> > chromosomeid;
>> >
>> >
>> >
>> >
>> >
>> >  count | chromosomeid
>> >
>> > -------+--------------
>> >
>> >  18856 |
>> >
>> >   1346 |    546000003
>> >
>> >    594 |    546000021
>> >
>> >    541 |    546000020
>> >
>> >    808 |    546000007
>> >
>> >    595 |    546000013
>> >
>> >   1632 |    546000011
>> >
>> >    505 |    546000019
>> >
>> >    554 |    546000012
>> >
>> >   1183 |    546000009
>> >
>> >   1662 |    546000004
>> >
>> >    706 |    546000016
>> >
>> >    613 |    546000014
>> >
>> >    693 |    546000015
>> >
>> >    822 |    546000023
>> >
>> >   1283 |    546000005
>> >
>> >   1274 |    546000006
>> >
>> >    751 |    546000010
>> >
>> >    578 |    546000017
>> >
>> >   2821 |    546000002
>> >
>> >   1286 |    546000008
>> >
>> >    648 |    546000018
>> >
>> > (22 rows)
>> >
>> >
>> >
>> > production-rat=# select count(*), chromosomeid from qtl group by
>> > chromosomeid;
>> >
>> >  count | chromosomeid
>> >
>> > -------+--------------
>> >
>> >   1774 |
>> >
>> > (1 row)
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > ======================
>> >
>> > Andrew Vallejos
>> >
>> > Web Developer II
>> >
>> > Biotechnology and Bioengineering Center
>> >
>> > Medical College of Wisconsin
>> >
>> > 414-955-4104
>> >
>> > [hidden email]
>> >
>> >
>> >
>> > _______________________________________________
>> > 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
>
>
>
>



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Re: Qtls and Chromosomes

Vallejos, Andrew
Yeah...that just dawned on be after I sent that email.  

-----Original Message-----
From: [hidden email] [mailto:[hidden email]]
Sent: Monday, November 22, 2010 12:40 PM
To: Vallejos, Andrew
Cc: Intermine
Subject: RE: [InterMine Dev] Qtls and Chromosomes

The XML below will populate the QTL.location reference and the
QTL.location.locatedOn (which is a chromosome) reference but not
QTL.chromosome.

In the query below you were looking in the QTL table for chromosome ID.
You don't have that relationship in your XML file so QTL.chromosomeid
will
be empty after loading that source.

You can set this in your XML file or use the post-process
create-chromosome.

> Really?  Because looking at the Intermine.xml file...
>
>    <item id="0_26" class="" implements="QTL">
>       <attribute name="symbol" value="Eae5" />
>       <attribute name="primaryIdentifier" value="61324" />
>       <attribute name="name" value="Experimental allergic
> encephalomyelitis QTL 5" />
>       <attribute name="lod" value="13.0" />
>       <attribute name="trait" value="Brain/spinal cord inflammation"
/>

>       <collection name="publications">
>          <reference ref_id="0_25" />
>       </collection>
>       <reference name="organism" ref_id="0_1" />
>    </item>
>    <item id="0_27" class="" implements="Location">
>       <attribute name="end" value="24470522" />
>       <reference name="feature" ref_id="0_26" />
>       <reference name="locatedOn" ref_id="0_13" /> <!-- ref to
> Chromosome 12 -->
>       <attribute name="start" value="20932559" />
>    </item>
>
> I have a Location, which references the Chromosome and the QTL.
>
>
> -----Original Message-----
> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of
Alex

> Kalderimis
> Sent: Monday, November 22, 2010 11:33 AM
> To: [hidden email]
> Cc: Vallejos, Andrew; Intermine
> Subject: Re: [InterMine Dev] Qtls and Chromosomes
>
> Ah yes - that is the change I made in the qtl script (switching from
> unless to if on the chrom test - at present it will never set
> chromosomes).
>
> I haven't sorted out checking in (pushing) yet, due to technical
> difficulties, but I shall look at that now.
>
> Alex
>
> On Mon, 2010-11-22 at 17:23 +0000, [hidden email] wrote:
>> Hi Andrew,
>>
>> In the XML you sent the other day, I don't see the gene.chromosome or
>> QTL.chromosome relationships assigned.
>>
>> Which source sets those?  Or do you use the "create-chromosome"
>> post-process to fill those in?
>>
>> Cheers,
>> Julie
>>
>> > I've gone through all my keys, data script, Intermine-xml file, and
> run
>> > a clean-all, and I don't see anything wrong.
>> >
>> >
>> >
>> > I usually get the following results; sometimes I get chromosomes
for

>> > QTLs but not for genes.
>> >
>> >
>> >
>> > production-rat=# select count(*), chromosomeid from gene group by
>> > chromosomeid;
>> >
>> >
>> >
>> >
>> >
>> >  count | chromosomeid
>> >
>> > -------+--------------
>> >
>> >  18856 |
>> >
>> >   1346 |    546000003
>> >
>> >    594 |    546000021
>> >
>> >    541 |    546000020
>> >
>> >    808 |    546000007
>> >
>> >    595 |    546000013
>> >
>> >   1632 |    546000011
>> >
>> >    505 |    546000019
>> >
>> >    554 |    546000012
>> >
>> >   1183 |    546000009
>> >
>> >   1662 |    546000004
>> >
>> >    706 |    546000016
>> >
>> >    613 |    546000014
>> >
>> >    693 |    546000015
>> >
>> >    822 |    546000023
>> >
>> >   1283 |    546000005
>> >
>> >   1274 |    546000006
>> >
>> >    751 |    546000010
>> >
>> >    578 |    546000017
>> >
>> >   2821 |    546000002
>> >
>> >   1286 |    546000008
>> >
>> >    648 |    546000018
>> >
>> > (22 rows)
>> >
>> >
>> >
>> > production-rat=# select count(*), chromosomeid from qtl group by
>> > chromosomeid;
>> >
>> >  count | chromosomeid
>> >
>> > -------+--------------
>> >
>> >   1774 |
>> >
>> > (1 row)
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > ======================
>> >
>> > Andrew Vallejos
>> >
>> > Web Developer II
>> >
>> > Biotechnology and Bioengineering Center
>> >
>> > Medical College of Wisconsin
>> >
>> > 414-955-4104
>> >
>> > [hidden email]
>> >
>> >
>> >
>> > _______________________________________________
>> > 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
>
>
>
>



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Re: Qtls and Chromosomes

Richard Smith
If you include the post-process create-chromosome-locations-and-lengths:

<post-process name="create-chromosome-locations-and-lengths"/>

this will fill in the chromosome and chromosomeLocation references for
all features that have a single location on a chromosome.  This should
solve the problem without you changing your XML generation.



Richard.




Vallejos, Andrew wrote:

> Yeah...that just dawned on be after I sent that email.  
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]]
> Sent: Monday, November 22, 2010 12:40 PM
> To: Vallejos, Andrew
> Cc: Intermine
> Subject: RE: [InterMine Dev] Qtls and Chromosomes
>
> The XML below will populate the QTL.location reference and the
> QTL.location.locatedOn (which is a chromosome) reference but not
> QTL.chromosome.
>
> In the query below you were looking in the QTL table for chromosome ID.
> You don't have that relationship in your XML file so QTL.chromosomeid
> will
> be empty after loading that source.
>
> You can set this in your XML file or use the post-process
> create-chromosome.
>
>> Really?  Because looking at the Intermine.xml file...
>>
>>    <item id="0_26" class="" implements="QTL">
>>       <attribute name="symbol" value="Eae5" />
>>       <attribute name="primaryIdentifier" value="61324" />
>>       <attribute name="name" value="Experimental allergic
>> encephalomyelitis QTL 5" />
>>       <attribute name="lod" value="13.0" />
>>       <attribute name="trait" value="Brain/spinal cord inflammation"
> />
>>       <collection name="publications">
>>          <reference ref_id="0_25" />
>>       </collection>
>>       <reference name="organism" ref_id="0_1" />
>>    </item>
>>    <item id="0_27" class="" implements="Location">
>>       <attribute name="end" value="24470522" />
>>       <reference name="feature" ref_id="0_26" />
>>       <reference name="locatedOn" ref_id="0_13" /> <!-- ref to
>> Chromosome 12 -->
>>       <attribute name="start" value="20932559" />
>>    </item>
>>
>> I have a Location, which references the Chromosome and the QTL.
>>
>>
>> -----Original Message-----
>> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of
> Alex
>> Kalderimis
>> Sent: Monday, November 22, 2010 11:33 AM
>> To: [hidden email]
>> Cc: Vallejos, Andrew; Intermine
>> Subject: Re: [InterMine Dev] Qtls and Chromosomes
>>
>> Ah yes - that is the change I made in the qtl script (switching from
>> unless to if on the chrom test - at present it will never set
>> chromosomes).
>>
>> I haven't sorted out checking in (pushing) yet, due to technical
>> difficulties, but I shall look at that now.
>>
>> Alex
>>
>> On Mon, 2010-11-22 at 17:23 +0000, [hidden email] wrote:
>>> Hi Andrew,
>>>
>>> In the XML you sent the other day, I don't see the gene.chromosome or
>>> QTL.chromosome relationships assigned.
>>>
>>> Which source sets those?  Or do you use the "create-chromosome"
>>> post-process to fill those in?
>>>
>>> Cheers,
>>> Julie
>>>
>>>> I've gone through all my keys, data script, Intermine-xml file, and
>> run
>>>> a clean-all, and I don't see anything wrong.
>>>>
>>>>
>>>>
>>>> I usually get the following results; sometimes I get chromosomes
> for
>>>> QTLs but not for genes.
>>>>
>>>>
>>>>
>>>> production-rat=# select count(*), chromosomeid from gene group by
>>>> chromosomeid;
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>  count | chromosomeid
>>>>
>>>> -------+--------------
>>>>
>>>>  18856 |
>>>>
>>>>   1346 |    546000003
>>>>
>>>>    594 |    546000021
>>>>
>>>>    541 |    546000020
>>>>
>>>>    808 |    546000007
>>>>
>>>>    595 |    546000013
>>>>
>>>>   1632 |    546000011
>>>>
>>>>    505 |    546000019
>>>>
>>>>    554 |    546000012
>>>>
>>>>   1183 |    546000009
>>>>
>>>>   1662 |    546000004
>>>>
>>>>    706 |    546000016
>>>>
>>>>    613 |    546000014
>>>>
>>>>    693 |    546000015
>>>>
>>>>    822 |    546000023
>>>>
>>>>   1283 |    546000005
>>>>
>>>>   1274 |    546000006
>>>>
>>>>    751 |    546000010
>>>>
>>>>    578 |    546000017
>>>>
>>>>   2821 |    546000002
>>>>
>>>>   1286 |    546000008
>>>>
>>>>    648 |    546000018
>>>>
>>>> (22 rows)
>>>>
>>>>
>>>>
>>>> production-rat=# select count(*), chromosomeid from qtl group by
>>>> chromosomeid;
>>>>
>>>>  count | chromosomeid
>>>>
>>>> -------+--------------
>>>>
>>>>   1774 |
>>>>
>>>> (1 row)
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ======================
>>>>
>>>> Andrew Vallejos
>>>>
>>>> Web Developer II
>>>>
>>>> Biotechnology and Bioengineering Center
>>>>
>>>> Medical College of Wisconsin
>>>>
>>>> 414-955-4104
>>>>
>>>> [hidden email]
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>>
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>>
>
>
>
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