[Bioperl-l] Drawing sequences in the "other" direction

[hz5 at njit.edu]

Michael,
This is what I did to solve this problem:
I will have one panel render +1 seq, then use another panel to render the -1 
seq in the "flipped" direction, then use copy to join the 2 panel into one 
picture.

haibo

Quoting "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk>:

> 
> 
> Hi Lincoln, List
> 
> Yeah, flip works great on the whole panel, but I have my top track which
> is a genome in the +1 direction, then I want to add another track which
> is a second genome, aligned to the first, but it runs in the -1
> direction, I want to flip the second track but not the first...
> 
> Would running through all the features and re-jigging the co-ordinates
> of all the features work?  I was hoping to avoid it... though I guess
> somewhere buried in the guts of Bio::Graphics::Panel, this code must
> already be written...?
> 
> Mick
> 
> 
> 
> -----Original Message-----
> From:	Lincoln Stein [mailto:lstein at cshl.edu]
> Sent:	Sun 19/06/2005 6:12 PM
> To:	bioperl-l at portal.open-bio.org
> Cc:	michael watson (IAH-C)
> Subject:	Re: [Bioperl-l] Drawing sequences in the "other" direction
> 
> Hi Michael,
> 
> Have you tried passing -flip=>1 to Bio::Graphics::Panel->new()?
> 
> Lincoln
> 
> On Tuesday 24 May 2005 08:16 am, michael watson (IAH-C) wrote:
> > Hi
> >
> > I'm trying to draw images of bits of aligned bacterial genomes with
> the
> > genes marked on as features.  Reasonably often a gene in one species
> is
> > on the +1 strand, and in another species it's on the -1 strand.  I
> want
> > to draw an image of these genes "aligned", one on top of the other,
> both
> > facing in the same direction (obviously those that I have flipped I
> will
> > annotate as such).
> >
> > I have been drawing images using Bio::Graphics::Panel and the
> add_track
> > method, but I can't figure out how to draw the sequence, and all
> it's
> > features, running in the opposite direction.  In fact, I doubt there
> is
> > one unless someone can point it out?
> >
> > I did think of drawing them in the right orientation and using the
> linux
> > "convert" command to flip the image, but then all the text is
> backwards!
> >
> > Any help appreciated
> >
> > Mick
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> 
> 
> 
> 
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> 



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Haibo Zhang, PhD
Computational Biology
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