[Bioperl-l] **Fwd: Re: SOLVED ver2 Bio::Graphics::Panel make ruler have neg values

Kevin Lam Koiyau ULNJUJERYDIX at spammotel.com
Thu Jun 1 02:53:46 EDT 2006


 Thanks Lincoln! Your code worked in ver 1.4 as well.
think the prob i had was due to me just adapting from the blast output
tutorial so i had something like
my $feature =
Bio::SeqFeature::Generic->new(-display_name=>$name,-score=>$score,-start=>$start,-end=>$end,
-source=>$source);

and maybe also because I didn't have the + sign for the numbers

on a side note, I think that the ability to offset the ruler might prove
useful for some applications. Will spend more time to understand the
$relative_coords_offset option in the arrow.pm when i can afford to, and
perhaps help contribute an offset option to arrow.pm

cheers
kevin

Content-Disposition: inline
>
> Hi Kevin,
>
> Since you are modifying the Panel.pm source code, why don't you just go
> ahead
> and use the current Bio::Graphics development tree? Since 1.5.1 it
> supports
> negative coordinates. Here's an illustration:
>
> #!/usr/bin/perl
>
> use strict;
>
> use Bio::Graphics;
> use Bio::Graphics::Feature;
>
> my $whole   = Bio::Graphics::Feature->new(-start=>-200,-end=>+200);
> my $feature =
> Bio::Graphics::Feature->new(-start=>-100,-end=>+100,-strand=>+1);
> my $panel   = Bio::Graphics::Panel->new(-start=> -200,
>                                          -end  => +200,
>                                          -width=>800,
>                                          -pad_left=>10,
>                                          -pad_right=>10);
> $panel->add_track($whole,
>                    -glyph=>'arrow',
>                    -double=>1,
>                    -tick=>2);
> $panel->add_track($feature,
>                   -glyph=>'box',
>                    -stranded=>1);
> print $panel->png;
>
> exit 0;
>
> The resulting image is attached.
>
> Lincoln
>
> On Tuesday 30 May 2006 23:45, Kevin Lam Koiyau wrote:
> > I am so sorry for the truncated email accidentally hit reply.
> > if anyone is interested i have opted to change
> >
> > change line 161 of arrow.pm in Perl/site/lib/Bio/Graphics/Glyph/arrow.pm
> > in linux its
> > /usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Glyph/arrow.pm
> >
> >
> >       $gd->string($font,$middle,$center+$a2-1,$label,$font_color)
> >
> > to
> >
> >       $gd->string($font,$middle,$center+$a2-1,$label-1000,$font_color)
> >
> > just  for this one-off use.
> >
> >
> >
> > strangely I found at line 112 for ver 1.51 bioperl in arrow.pm a hidden
> > option for coords offset?
> >     my $relative_coords_offset =
> $self->option('relative_coords_offset');
> >     $relative_coords_offset    = 1 unless defined
> $relative_coords_offset;
> > but entering the option -relative_coords_offset=>1000 in the arrow
> glyphs
> > didn't do anything...
> >
> >
> >
> > 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
> > > > >
> > > > > _______________________________________________
> > > > > Bioperl-l mailing list
> > > > > Bioperl-l at lists.open-bio.org
> > > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > > >
> > > > --
> > > > 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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> > >
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> >
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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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