Re: [XMLPipeDB-developer] create custom profile for S. aureus COL

[John D. N. D. <do...@lm...>]

Greetings Sarah,

I have uploaded a new version of GenMAPP Builder, version 2.0b81, which includes a custom species profile for S. aureus COL.  This version adds the taxon ID that you requested plus sets the custom link pattern.

With regard to tally engine behavior, I need to dig a bit further before determining the proper fix.  I figure that the discrepancy of two is due to two ordered locus records that are "slashed" IDs---i.e., they really are two IDs in a single "record," and thus both XML and PostgreSQL count them once.  However, GenMAPP export separates them, and they thus add to the OrderedLocusNames count.

I downloaded and searched the XML file for S. aureus COL (newer than what you have by a few days) and found the following "slashed" IDs:

    <name type="ordered locus">SACOL0317/SACOL0390</name>
    <name type="ordered locus">SACOL0081/SACOL0082</name>

There are indeed two of them---explaining why OrderedLocusNames increases by 2 upon export.  If this is what we want Tally Engine to take into account, then I will work to modify it accordingly then post a new version when ready.

Meanwhile, I hope the new export profile creates a GenMAPP Gene Database file that is better suited for your study.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Sep 16, 2014, at 9:29 AM, Sarah Patno <sp...@li...> wrote:

> Hi Dr. Dionisio,
> 
> Please create a custom profile for this Taxon ID: 93062. 
> 
> The link out for OrderedLocusNames should be to this:
> 
> http://ensemblgenomes.org/id/~
> 
> Thank you,
> Sarah Patno
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