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

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Sun Jun 19 14:18:07 EDT 2005

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...?


-----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()?


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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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

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