[Gmod-help] polypeptide view in Gbrowse

[Scott Cain]

Hi Lincoln and Newton,

I was under the impression that the draw_protein option was
incompletely implemented, but if it works with other database
adaptors, perhaps there is a bug in the Chado GBrowse adaptor.  Have
you tried the cds glyph, which should display residues when zoomed in
far enough?  If draw_protein doesn't work but the cds glyph does, it
indicates a Bio::Graphics problem.  If neither work, it is more likely
a Chado adaptor or data problem.

As for the T. cruzi problem--I don't see anything in the data that
looks problematic.  Where there any error messages while loading or in
the apache error_log (with a preemptive note: error messages about
Bio::Graphics::BrowserConfig don't mean anything)?

Scott


On Tue, Dec 16, 2008 at 3:35 PM, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Newton,
>
> Have you tried passing the draw_protein option?
>
>  [Polypeptide]
>  feature = polypeptide
>  glyph   = transcript
>  draw_protein = 1
>
> Also check out the "protein" and "translation" glyphs.
>
> The T. cruzi problem sounds like a chado issue -- I will defer to Scott
> and/or David on this.
>
> Best,
>
> Lincoln
>
> On Tue, Dec 16, 2008 at 2:01 PM, Newton Vidal <nwvidal at gmail.com> wrote:
>>
>> Dear all,
>>
>> I am starting to work with GMOD and Chado, and I have uploaded genbank
>> files from five different protozoan genomes, using bp_genbank2gff3.pl and
>> gmod_bulk_load_gff3.pl scripts in our local chado v. 1.0 database.
>>
>> I have run into two major problems when visualizing data with Gbrowse v.
>> 1.69:
>>
>> ·        The polypeptide feature shows nucleic acid sequence instead of
>> amino acid, when clicked;
>> ·        For four of the genomes (Leishmania sp. and Trypanosoma brucei)
>> the others features work fine, but for T. cruzi, no data is provided when I
>> click its features.
>>
>> I have edited chado.conf file to work with my database and added the lines
>> below:
>>
>> [Polypeptide]
>> feature      = polypeptide
>> glyph        = transcript
>> height       = 10
>> key          = Polypeptide
>> bgcolor      = green
>>
>> I'm sending attached T. brucei and T. cruzi's GFF files and gbrowse conf
>> file. I have a 80MB dump file and I can share it if needed.
>>
>> Thanks in advance,
>>
>> Newton Vidal
>
>
>
> --
> Lincoln D. Stein
>
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>



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