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

[hz5 at njit.edu]

Hi Michael,
I have the cooresponding code here, hope it will help:

foreach my $p(@allpanel){
        my $tim = GD::Image->new($p->width(), $p->height());
        $p->gd($tim);
        $gdImg->copy($tim, $0, $hid, 0, 0, $p->width(), $p->height());
        $hid += $p->height();
}
my $pngData = $gdImg->png();
haibo
//cheers

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

> Hi Haibo
> 
> Sorry, is "copy" a bioperl function or a linux/windows one?  I tried
> this using an external linux command, but it had trouble figuring out
> what size the images were
> 
> Mick
> 
> -----Original Message-----
> From: hz5 at njit.edu [mailto:hz5 at njit.edu] 
> Sent: 20 June 2005 03:20
> To: michael watson (IAH-C)
> Cc: bioperl-l at portal.open-bio.org
> Subject: RE: [Bioperl-l] Drawing sequences in the "other" direction
> 
> 
> 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
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > 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/
> Share postdoc information in cyberspace. Welcome your stories,
> suggestions and 
> advice!
> 



=========================================================
Haibo Zhang, PhD
Computational Biology
http://www.cyberpostdoc.org/
Share postdoc information in cyberspace. Welcome your stories, suggestions and 
advice!