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

[Lincoln Stein]

That's the exact solution I would have proposed.

Lincoln

On Sunday 19 June 2005 10:19 pm, hz5 at njit.edu wrote:
> 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
> > >
> > > _______________________________________________
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> > > 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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> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> =========================================================
> Haibo Zhang, PhD
> Computational Biology
> http://www.cyberpostdoc.org/
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724