[Bioperl-l] Re: Bioperl-l Digest, Vol 4, Issue 3

[Scott Cain]

Laurence,

I ran a script very similar to what you are using (the code I used is
below), and I didn't have any problems, at least not if what is expected
is the same as this: http://www.gmod.org/BioGraphicsTest.png.

I suspect you are having a version problem.  I am using bioperl-live
(from CVS), but when I installed bioperl-1.2.2, it failed in the way you
describe.  Where is the tutorial you are reading?  Perhaps it is not in
sync with the most recent version of released bioperl.

Here is the script I used:
#!/usr/local/bin/perl -w

use strict;
use Bio::Graphics;
use Bio::SeqFeature::Generic;

my $panel= Bio::Graphics::Panel->new(-length =>1000,-width =>800);
my $track=$panel->add_track(-glyph =>'generic',-label =>1);

while (<DATA>)
{
         chomp;
         next if /^\#/;
         my ($name,$score,$start,$end)=split /\s+/;
         warn "$name\n";
         my $feature=
Bio::SeqFeature::Generic->new(-display_name=>$name,-score=>$score,-start=>$start,-end=>$end);
         $track->add_feature($feature);
}

print $panel->png;

__DATA__
#hit    score   start   end
truc1   381     2       200
truc2   210     2       210
truc3   800     2       200
truc4   1000    380     921
truc5   812     402     972
truc6   1200    400     970
bum     400     300     620
pres1   127     310     700

Scott

On Wed, 2003-08-06 at 13:31, bioperl-l-request at portal.open-bio.org
wrote:
> I try to learn how to use the module Bio::Graphics.
> I found he How To from Lincoln Stein on the web. I try to practice with the 
> examples, it's working except for the labels of the features that don't 
> appear on my figure.
> Does anybody ever use this module?

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory