[Bioperl-l] Problem rendering a BLAST result

[Scott Cain]

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
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