Re: [gmod-cmap] importing a .gff

[Ken Youens-C. <kyc...@gm...>]

On Jun 14, 2009, at 5:31 PM, Andrew Couperthwaite wrote:

> Hi,
>
> I'm having trouble importing a .gff into cmap.  Using the
> cmap_admin.pl, I select import data, .gff, give it the file name (it
> says it reads it correctly) I select the species and map set and it
> goes to work reading in the data.  It reads in all the data and the
> purges the caches.
>
> When I check CMAP, it doesn't even display the species in the drop
> down menu.
>
> Looking at the database using DBVis, cmap_species table seems to
> contain the correct information, cmap_map_set seems to contain the
> correct information, but cmap_feature does not contain any of the
> features that it should have read in from the .gff file.
>
> The only differences I can see from when I imported data before and
> this time, is that this time i'm using a .gff rather than a cmap tab-
> delimited file and that this map is a 'physical' map rather than a
> 'genetic' one.
>
> Any thoughts?
>
> Thanks,
> -Andrew


Andrew,

Ben Faga wrote the GFF importer, and, unfortunately, he's no longer on  
the project.  I'm not sure to what extent this code was vetted, and  
I'm not familiar with the code myself.  I wonder if you have the data  
already in a tab-delimited format?  If so, can you just import it that  
way?  If not, what is the advantage for you to use GFF?

--
Ken Youens-Clark
kc...@cs...
Gramene.org Project Manager
Ware Lab/CSHL/USDA-ARS