[Bioperl-l] Problem rendering a BLAST result

[Scott Cain]

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
>>>
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>>
>>
>>
>> --
>> Luiz Thibério Rangel
>>
>
>
>
> --
> Luiz Thibério Rangel
>
> _______________________________________________
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> 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