[Bioperl-l] Hi

Barry Moore barry.moore at genetics.utah.edu
Thu Jun 12 17:44:29 EDT 2008


Did you really want to go backwards from gff3 to gff2 or did you mean  
from gff2 to gff3?

If you want to go from GTF/GFF2 forward to GFF3 there is a script  
available through the Sequence Ontology for doing this (http:// 
song.cvs.sourceforge.net/song/software/scripts/gtf2gff3/).  It  
handles a wide variety of GTF and GFF2 files, however since there is  
a lot of variability of implementations of those formats I can't  
guarantee that it will handle every flavor.  For example, it does not  
work on GTF from the UCSC
table browser because those files use the same ID for gene and  
transcript, so it is impossible to group multiple transcripts to a  
gene. The version released will has been tested on Ensembl and  
Twinscan GTF.  I happen to be working on extending that script right  
now to handle a GFF2/GFF3 hybrid found in WS180 release from WormBase  
so if it doesn't handle your case it may soon.  If you use it and  
have feedback I'd appreciate hearing from you.

Barry

Barry Moore
Senior Research Specialist
Eccles Institute of Human Genetics
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




On Jun 12, 2008, at 3:18 PM, veena bhonagiri wrote:

> Hi,
> I was looking for a parser to convert gff3 to gff2 format. Is there  
> one available?
>
> thanks,
> Veena
>
>
>
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