[Bioperl-l] Problem rendering a BLAST result
Luiz Thiberio Rangel
lthiberiol at gmail.com
Fri May 13 13:33:26 UTC 2011
Hi Scott,
thanks very much. It worked very well after replacing the Glyph.pm!
On Fri, May 13, 2011 at 12:05 AM, Scott Cain <scott at scottcain.net> wrote:
> Hi Luiz,
>
> There was a bug introduced in the last release of Bio::Graphics. If
> you replace your copy of Bio::Graphics::Glyph with the attached one,
> it should work.
>
> Scott
>
>
> On Thu, May 12, 2011 at 3:28 PM, Luiz Thiberio Rangel
> <lthiberiol at gmail.com> wrote:
> > 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
> >
>
>
>
> --
> ------------------------------------------------------------------------
> 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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