[Gmod-help] load QTL gff3 file for GBrowse

[Scott Cain]

Hi Zhiliang,

It is best to send questions like this (that is, anything to do with
GBrowse) to the GBrowse mailing list, as there are lots of active
readers of the list that can contribute to solutions.

Of the top of my head, I don't know why this isn't working, but I can
tell you that the file you linked to is not valid GFF3.  The separator
for tag value pairs in the ninth column should be an equals, and first
letter upper case tag are reserved, so for example, this ninth column
entry:

  Name="Birth Weight QTL 1288";QTL_ID:1288; Type:Significant; p-value
= 0.026;Varance = .688; Trait:Birth Weight; PubMed_ID:14753343

should look more like this:

  Name="Birth Weight QTL 1288";qtl_id=1288; type=Significant; p-value
= 0.026;varance = .688; trait=Birth Weight; Dbxref=PMID:14753343

I don't think that would necessarily cause the problem you are seeing
though.  If you fix that and it still doesn't work, I'll take a look.

Scott


On Wed, Oct 29, 2008 at 11:10 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
> Hi there,
>
> I have created a GFF file from my QTL data as in
> http://www.animalgenome.org/hu/share/tmp/QTLbt.txt
>
> and loaded it with
>  > cat QTLbt.txt | bp_fast_load_gff.pl -d gb_cattle -u xx -p xx -f -
>
> loading normalized group, type and attribute information...ok
> creating load file /usr/tmp/fdata.20452...ok
> pausing for 0.5 sec...ok
> opening load file for writing...ok
> creating load file /usr/tmp/ftype.20452...ok
> pausing for 0.5 sec...ok
> opening load file for writing...ok
> creating load file /usr/tmp/fgroup.20452...ok
> pausing for 0.5 sec...ok
> opening load file for writing...ok
> creating load file /usr/tmp/fdna.20452...ok
> pausing for 0.5 sec...ok
> opening load file for writing...ok
> creating load file /usr/tmp/fattribute.20452...ok
> pausing for 0.5 sec...ok
> opening load file for writing...ok
> creating load file /usr/tmp/fattribute_to_feature.20452...ok
> pausing for 0.5 sec...ok
> opening load file for writing...ok
> Fast loading enabled
> Feature load time  0.00s
> Loading fasta file -
> -: 0 records loaded
> Fasta load time  0.02s
> Indexing and analyzing tables.  This may take some time (you may see
> database messages during the process)...
> gb_cattle.ftype analyze status  OK
> gb_cattle.fgroup        analyze status  OK
> gb_cattle.fattribute    analyze status  OK
> gb_cattle.fdata analyze status  OK
> gb_cattle.fattribute_to_feature analyze status  OK
> gb_cattle.fdna  analyze status  OK
> Total parse & load time  1.29s
> SUCCESS: 0 features successfully loaded
>
> It says "0 records loaded"/"0 features successfully loaded"
> -- Do you see any problem how could this happen?
> (BTW, my GBrowse is at http://www.animalgenome.org/cgi-bin/gbrowse/cattle)
>
> Any hint will be appreciated!
>
> Zhiliang
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research