[Gmod-help] Re: [Gmod-schema] Error loading GFF3 file into chado

[Scott Cain]

Hi Manny,

If you have GFF2, you will need to convert it to GFF3, but there is no  
simple tool for doing that, so it may be difficult.  The format of  
this file is relatively straight forward, so it may not be too hard.

Scott


On Aug 13, 2009, at 6:23 PM, Dave Clements, GMOD Help Desk wrote:

> Hi Manny,
>
> Did you get the GFF file from
> http://genome.jgi-psf.org/Sorbi1/Sorbi1.download.ftp.html ?
>
> I downloaded ftp://ftp.jgi-psf.org/pub/JGI_data/Sorghum_bicolor/v1.0/Sorbi1_GeneModels_Sbi1_4_Sbi1_4.gff.gz
> and it was a GFF2 file, which may cause a problem for the load_gff3
> script.  Try using ....
>
> Um, I don't know what you use to load GFF2 into Chado.  Does anybody  
> know?
>
> A second problem:  The file I downloaded does not contain "super_10"
> anywhere.  (I assume that you downloaded one of the others?)  However,
> I've still got a guess  The file I downloaded does not define any
> chromosome/contig wide features.   You'll need to write a script to
> derive the length of each chromosome/contig/scaffold in the file, and
> then define GFF2 lines for each, that span the whole length of the
> chrom/contig/scaffold.
>
> Does that make sense?
>
> Thanks,
>
> Dave C
>
> On Tue, Aug 4, 2009 at 11:06 AM, Manuel J. Torres<mjtorres at uga.edu>  
> wrote:
>> I get the following error loading my sorted sorghum GFF3
>> file (DOE JGI v1.4) into chado using gmod_bulk_load_gff3.pl:
>>
>> "Unable to find srcfeature super_10 in the database."
>>
>> Manny Torres, PGML-UGA
>>
>>
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>
>
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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research