[Bioperl-l] **Fwd: Re: URGENT: Bio::Graphics::Panel make the ruler have

[Lincoln Stein]

Hi Kevin,

I'm afraid that there is no offset value. You'll need the 1.51 version of 
bioperl to handle negative numbers properly. I understand your reluctance to 
upgrade just to get the Bio::Graphics functionality. You might consider 
checking out just the Bio/Graphics subtree and installing that. It should 
work on top of 1.4

Lincoln

On Monday 29 May 2006 05:46, Kevin Lam Koiyau wrote:
> Hi!
> oh it was in a slightly different header asking about the create image map
> feature.
> I am using the stable version 1.4 of bioperl now. In any case I have not
> added the sequence as a feature annotated seq. as I already have the bp
> where the TF binds (in 1-1050 numberings) so what I did was to just add
> graded segments based on the position.
> I saw that there is a scale function for the arrow glyp however, it is a
> multiply function, can it be hacked to take in a offset value (ie minus the
> scale by 1000?)
>
> cheers
> kevin
>
>
> Hi,
>
> > For some reason I didn't see the first posting on this. In current
> > bioperl live, the ruler can have negative numberings - I use this
> > routinely. You need
> > to create a feature that starts in negative coordinates. What is
> > happening to
> > you when you try this?
> >
> > Lincoln
> >
> > On Wednesday 24 May 2006 21:59, Kevin Lam Koiyau wrote:
> > > Hi
> > > thanks for the help offered thus far!
> > > sigh I am trying to annotate TFBS on a -1000 to +50 bp promtoer seq
> >
> > using
> >
> > > bioperl. therefore i was asked to make the numberings as such (-1000)
> > > is there any way at all to do this in bioperl without changing the .pm
> >
> > file?
> >
> > > thanks guys..
> > > kevin
> > >
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> > --
> > Lincoln D. Stein
> > Cold Spring Harbor Laboratory
> > 1 Bungtown Road
> > Cold Spring Harbor, NY 11724
> > (516) 367-8380 (voice)
> > (516) 367-8389 (fax)
> > FOR URGENT MESSAGES & SCHEDULING,
> > PLEASE CONTACT MY ASSISTANT,
> > SANDRA MICHELSEN, AT michelse at cshl.edu
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING, 
PLEASE CONTACT MY ASSISTANT, 
SANDRA MICHELSEN, AT michelse at cshl.edu