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

[Jason Stajich]

yes I know - that is why I fixed that script in CVS just now.  'you'  
was meant generally - fault of the script and API drifting apart so  
not your (Mick) fault at all.

-j
On May 9, 2005, at 3:11 PM, michael watson ((IAH-C)) wrote:

> 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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>> Bioperl-l at portal.open-bio.org
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>>
>>
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