[Genome] gff to flyBaseGene.txt

[Angie Hinrichs]

Hi Karen,

We do have a script... but it evolves quickly.  Most new FlyBase 
annotation releases include GFF3 that uses slightly different keywords 
from the previous releases.  Even Dmel 5.3 had several differences 
from 5.1.  So the script changes almost every time.  With that caveat, 
attached is the version of the script used for Dmel 5.3.  It might 
work for the release you have in mind, or might require some tweaks.

Our source tree includes more detailed instructions for building that 
track, and in fact all tracks in dm3 (Dmel Release 5), in the file 
kent/src/hg/makeDb/doc/dm3.txt.  Search for the section that begins 
with "FLYBASE 5.3 ANNOTATIONS".  It includes some UNIX commands that 
summarize keyword usage, and shows how the script is used.

Hope that helps, and please send more questions to genome at soe.ucsc.edu 
if you have them,

Angie

On Mon, 17 Dec 2007, Karen M. Wong wrote:

> Hi,
> 
> Since it seems that updates are only made to your D.mel annotation
> files after major FlyBase releases, I was wondering if you had a
> script, or directions on how to go about creating "flyBaseGene.txt"
> files from current release versions of .gff files?
> 
> Much thanks,
> Karen
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