[Bioperl-l] Problems with Bio/Graphics/Feature.pm

[michael watson (IAH-C)]

Hi

I didn't deliberately pass a RichSeq object - a call in the render_sequence.pl script did i.e. render_sequence.pl doesn't work "out of the box".

I think it's this piece of code that breaks it:

$panel->add_track(arrow => $seq,
  -bump => 0,
  -double=>1,
  -tick => 2);

Mick
:-)

-----Original Message-----
From:	Jason Stajich [mailto:jason.stajich at duke.edu]
Sent:	Mon 09/05/2005 7:27 PM
To:	michael watson (IAH-C)
Cc:	bioperl-l at portal.open-bio.org
Subject:	Re: [Bioperl-l] Problems with Bio/Graphics/Feature.pm

you need to pass in a SeqFeature::Generic or Graphics::Feature obj  
instead of Sequence object.

I updated the code in CVS:

http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/ 
examples/biographics/render_sequence.pl?rev=1.2&cvsroot=bioperl

[fyi Bio::DB Bio::Graphics developers]
There was something else weird about how this was working - somehow  
Bio::Location objects are getting passed to the description and label  
functions.  I don't quite understand, might be my local code playing  
too.

-jason
On May 9, 2005, at 6:29 AM, michael watson ((IAH-C)) wrote:

> Hi
>
> I'm hacking around with the render_sequence.pl example script and keep
> getting errors:
>
> Can't locate object method "seq_id" via package "Bio::Seq::RichSeq" at
> /usr/local/bioperl-1.5.0/Bio/Graphics/Feature.pm line 269, <DATA> line
> 191.
>
> I also get a similar message about not being able to locate object
> method "start", which is called on the next line of
> Bio::Graphics::Feature.pm
>
> I vaguely recall asking about this previously - was a solution ever
> presented?
>
> Many thanks in advance
>
> Mick
>
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