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

[Lincoln Stein]

Thanks to Jason for fixing that. I'm afraid that I've been partly responsible 
for the drift.

Lincoln

On Monday 09 May 2005 03:54 pm, Jason Stajich wrote:
> 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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>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724