Hi Heekim,
I agree that the loader should have warned you that there was a problem.
I modified the loader so that if it detects items in the GFF file that
make it look like computational analysis results, it warns the user.
These items include Target attributes, scores or types that contain the
word 'match'.
Thanks for your perseverance,
Scott
On Tue, 2008-02-26 at 13:12 -0800, heekim wrote:
> Dr. Gilber,
>
> Thank you for your consideration.
>
> Isabelle, one of GBROWSE users, informed me how to figure out this issue
> before you let me know.
> All of you pointed out --analysis option.
>
> I followed her direction,
> insert into analysis (name,program,programversion)
> values('NGS_probe','Gmap','NGS');
> then
> I ran /usr/local/bin/gmod_bulk_load_gff3.pl --dbname BeetleBaseTest
> --organism beetle --gfffile tcas3_ChrLGX_probe.gff3 --analysis NGS_probe
>
> it worked well.
>
> I would like to point out that I thought that the option seemed to be used
> for some special features such as match or EST_match. If I don't use the
> option for the features, gmod_bulk_load_gff3.pl stops running process then
> display its error message.
>
> Unlikely, in my case, gmod_bulk_load_gff3.pl do not provide the error
> message. It was so difficult to find out what was wrong. I never recognized
> that I have to use the analysis option.
>
> Thank you for all of you.
>
> Hee Shin
>
>
>
>
> Don Gilbert-6 wrote:
> >
> >
> > Hee Shin,
> >
> >
> > Here is a suggestion, if you haven't tried it. Be warned that I haven't
> > tried it.
> > Using these load options:
> > gmod_bulk_load_gff3.pl --analysis=NimbleScan.dataset1 NimbleScan.gff3
> > gmod_bulk_load_gff3.pl --analysis=NGS_probe.dataset1 NGS_probe.gff3
> >
> > should load the data to chado analysisfeatures with these columns:
> > table analysis.program=NimbleScan, .source=dataset1
> > table analysis.program=NGS_probe, .source=dataset1
> > table analysisfeature.significance=GFF.score
> >
> > and the gbrowse chado adaptor should then find feature.score from
> > analysisfeature.significance column.
> >
> > This may also change the GFF feature.source values for gbrowse.conf
> > (I'm not sure):
> > > feature = microarray_oligo:NimbleScan.dataset1
> > > feature = region:NGS_probe.dataset1
> >
> > You don't need to add the .dataset1 source name for the analysis. But
> > that would be good practice in case you want to add
> > NimbleScan.dataset2, .dataset3, etc.
> >
> >
> > - Don
> > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> > -- [EMAIL PROTECTED]://marmot.bio.indiana.edu/
> >
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> >
> >
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. [EMAIL PROTECTED]
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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