[Gmod-tripal-devel] possible small glitch in GFF import with automatic feature name

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] possible small glitch in GFF import with automatic feature name

Michael Dondrup-3
I am looking at few features that have been imported from GFF files in Tripal. If the feature doesn't have name or ID
attribute it gets an automatically assigned name including the start and end coordinates. However the start in
the generated name seems to be off by 1, e.g.:
when I look at a feature in gbrowse:
maker-LSalAtl2s2-augustus-gene-14.11-mRNA-1-CDS-LSalAtl2s2-1375784240:1331843..1331944 class=Sequence position=LSalAtl2s2:1331844..1331944 (+ strand)

The position displayed by gbrowse and the import are seemingly correct compared to the GFF file, so only the name is affected.

Michael


------------------------------------------------------------------------------
Introducing Performance Central, a new site from SourceForge and
AppDynamics. Performance Central is your source for news, insights,
analysis and resources for efficient Application Performance Management.
Visit us today!
http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] possible small glitch in GFF import with automatic feature name

Stephen Ficklin-2
Hi Michael,

Good catch.   In Chado, the coordinates are zero-based, so the start
coordinate will be subtracted by 1 when storing.  But, you are right, it
makes more sense for the generic name to have the start coordinate as
specified in the GFF file not the zero-indexed value.

I have fixed the code in the 6.x-1.x development branch to add 1 to the
start coordinate when constructing the generic name.

Stephen

On 8/19/2013 11:44 AM, Michael Dondrup wrote:

> I am looking at few features that have been imported from GFF files in Tripal. If the feature doesn't have name or ID
> attribute it gets an automatically assigned name including the start and end coordinates. However the start in
> the generated name seems to be off by 1, e.g.:
> when I look at a feature in gbrowse:
> maker-LSalAtl2s2-augustus-gene-14.11-mRNA-1-CDS-LSalAtl2s2-1375784240:1331843..1331944 class=Sequence position=LSalAtl2s2:1331844..1331944 (+ strand)
>
> The position displayed by gbrowse and the import are seemingly correct compared to the GFF file, so only the name is affected.
>
> Michael
>
>
> ------------------------------------------------------------------------------
> Introducing Performance Central, a new site from SourceForge and
> AppDynamics. Performance Central is your source for news, insights,
> analysis and resources for efficient Application Performance Management.
> Visit us today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


------------------------------------------------------------------------------
Introducing Performance Central, a new site from SourceForge and
AppDynamics. Performance Central is your source for news, insights,
analysis and resources for efficient Application Performance Management.
Visit us today!
http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel