Probe Sequences

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Probe Sequences

Vallejos, Andrew

Example Probe: 1367459_at

 

I am loading probe sequence into RatMine, however when I click on the sequence table I get length of 0, the fast button throws an internal server error, and if I go to a Sequence record the page is not displayed correctly, with the residues appearing on the right hand side of the page.

 

Any suggestions on where my error is?

 

Thanks,

 

Andrew

 

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

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


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Re: Probe Sequences

Julie Sullivan
Hi Andrew,

There are a couple issues with sequences for probes:

1. sequence.length = 0

175477 of 206278 sequences have a length of zero.  I'm not sure what's causing
this.  Do you set that value in the converter, and it's getting overwritten?  Or
do you leave that value empty?

2. FASTA link throws an error

That's an InterMine bug, I've put in a ticket.  This will be fixed in the next
InterMine release.

We don't have any objects with a collection of sequences so we never had this
problem before.  FlyMine's probesets have a collection of locations instead as
we don't have the sequences.

3. residues appearing on the right hand side of the page.

"Sequence.residues" has been specifically configured to appear on the right side
of the page.  The webconfig-model.xml file is the file which controls how data
is displayed in your webapp.  If you update the entry on "Sequence", you can
update where the residues appear on the report page.  Here are the docs on that
file:

        http://intermine.org/wiki/WebConfigModel

Specifically, "showOnRight" is what you want to remove.

Cheers,
Julie

Vallejos, Andrew wrote:

> Example Probe: 1367459_at
>
>  
>
> I am loading probe sequence into RatMine, however when I click on the
> sequence table I get length of 0, the fast button throws an internal
> server error, and if I go to a Sequence record the page is not displayed
> correctly, with the residues appearing on the right hand side of the
> page.
>
>  
>
> Any suggestions on where my error is?
>
>  
>
> Thanks,
>
>  
>
> Andrew
>
>  
>
> ======================
>
> 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]
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