[Bioperl-l] Problem rendering a BLAST result

[Luiz Thiberio Rangel]

The problem is not a specific BLAST result. Anyway, I'm attaching a small
one.

Thank you, again...

On Thu, May 12, 2011 at 4:08 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Luiz,
>
> If you could also send the blast file that is causing the problem,
> that would help too.  I don't have one handy to test with.
>
> Scott
>
>
> On Thu, May 12, 2011 at 1:34 PM, Luiz Thiberio Rangel
> <lthiberiol at gmail.com> wrote:
> > I've been using the same code used in the BioPerl's HOWTO (
> > http://www.bioperl.org/wiki/Render_blast4) and even if the "-bgcolor"
> > definition  is removed the error persists.
> >
> > The same script is working well into a older version of the bioperl, but
> I
> > can't find where is the problem.
> >
> >
> > best regards
> >
> > On Tue, May 10, 2011 at 9:14 PM, Luiz Thiberio Rangel
> > <lthiberiol at gmail.com>wrote:
> >
> >> The code is this one -->
> >> http://www.bioperl.org/wiki/HOWTO:Graphics#Parsing_Real_BLAST_Output.
> The
> >> same used in this example.
> >>
> >>
> >> On Tue, May 10, 2011 at 5:55 PM, Kevin Brown <Kevin.M.Brown at asu.edu
> >wrote:
> >>
> >>> Would help if we can see your code as line 68 of yeah.pl is the final
> >>> line of the script you linked.
> >>>
> >>> It is trying to set the bgcolor based on a value that it thinks should
> >>> be held in the Bio::SeqFeature::Generic object as a tag, but no such
> tag
> >>> exists.
> >>>
> >>> > -----Original Message-----
> >>> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >>> > bounces at lists.open-bio.org] On Behalf Of lthiberiol
> >>> > Sent: Tuesday, May 10, 2011 6:21 AM
> >>> > To: bioperl-l at bioperl.org
> >>> > Subject: [Bioperl-l] Problem rendering a BLAST result
> >>> >
> >>> > Hi...
> >>> >
> >>> > I've been trying to parse a BLAST output and generate a figure based
> >>> > on it's result. I'm using this example (http://www.bioperl.org/wiki/
> >>> > HOWTO:Graphics#Parsing_Real_BLAST_Output), but when I execute it i
> get
> >>> > the following error message:
> >>> >
> >>> > ------------- EXCEPTION: Bio::Root::Exception -------------
> >>> > MSG: asking for tag value that does not exist bgcolor
> >>> > STACK: Error::throw
> >>> > STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/
> >>> > Root.pm:368
> >>> > STACK: Bio::SeqFeature::Generic::get_tag_values
> /usr/local/share/perl/
> >>> > 5.10.1/Bio/SeqFeature/Generic.pm:517
> >>> > STACK: Bio::Graphics::Glyph::bgcolor
> /usr/local/share/perl/5.10.1/Bio/
> >>> > Graphics/Glyph.pm:703
> >>> > STACK: Bio::Graphics::Glyph::graded_segments::bgcolor
> >>> /usr/local/share/
> >>> > perl/5.10.1/Bio/Graphics/Glyph/graded_segments.pm:124
> >>> > STACK: Bio::Graphics::Glyph::graded_segments::draw /usr/local/share/
> >>> > perl/5.10.1/Bio/Graphics/Glyph/graded_segments.pm:59
> >>> > STACK: Bio::Graphics::Glyph::track::draw
> /usr/local/share/perl/5.10.1/
> >>> > Bio/Graphics/Glyph/track.pm:35
> >>> > STACK: Bio::Graphics::Panel::gd /usr/local/share/perl/5.10.1/Bio/
> >>> > Graphics/Panel.pm:588
> >>> > STACK: Bio::Graphics::Panel::png /usr/local/share/perl/5.10.1/Bio/
> >>> > Graphics/Panel.pm:1067
> >>> > STACK: yeah.pl:68
> >>> > -----------------------------------------------------------
> >>> >
> >>> > Thanks!
> >>> > _______________________________________________
> >>> > Bioperl-l mailing list
> >>> > Bioperl-l at lists.open-bio.org
> >>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>
> >>
> >>
> >> --
> >> Luiz Thibério Rangel
> >>
> >
> >
> >
> > --
> > Luiz Thibério Rangel
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Luiz Thibério Rangel
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