[Bioperl-l] Bio::Graphics

Mon Feb 14 21:51:46 UTC 2011

Hi,

We had recently updated BioPerl and Bio::Graphics and found some applications not working properly. As an example simple graphics script like:

#####################################################

use Bio::Graphics::Panel;
use Bio::SeqFeature::Generic;

use CGI;      # or any other CGI:: form handler/decoder

print "Content-type: text/html\n\n";

my $panel = Bio::Graphics::Panel->new(-length => 700,
                                      -width  => 700
                                      );

my $track = $panel->add_track(-glyph       => 'generic',
                              -label       => 1
                              );

my $feature = Bio::SeqFeature::Generic->new(-start        => 1,
                                            -end          => 400
                                            );
$track->add_feature($feature);

print "<html><body>TEST IMAGE:<br>";

open GRAPH, "> /srv/www/htdocs/tmp/test.png" or die "could not open image file";
print GRAPH $panel->png;
close(GRAPH);

print "<img src=\"/tmp/test.png\">";
print "</body></html>";

#####################################################

is giving following error when I debug:

  DB<1> n
Can't locate object method "attributes" via package "Bio::SeqFeature::Generic" at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line 703.
 at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line 703
        Bio::Graphics::Glyph::bgcolor('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)') called at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line 1299
        Bio::Graphics::Glyph::filled_box('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)', 'GD::Image=SCALAR(0x2002460)', 0, 0, 400, 7) called at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line 1471
        Bio::Graphics::Glyph::draw_component('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)', 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph/generic.pm line 347
        Bio::Graphics::Glyph::generic::draw_component('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)', 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line 1050
        Bio::Graphics::Glyph::draw('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)', 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph/generic.pm line 338
        Bio::Graphics::Glyph::generic::draw('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)', 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph/track.pm line 35
        Bio::Graphics::Glyph::track::draw('Bio::Graphics::Glyph::track=HASH(0x1d5bb10)', 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Panel.pm line 588
        Bio::Graphics::Panel::gd('Bio::Graphics::Panel=HASH(0x1b1f6b0)') called at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Panel.pm line 1067
        Bio::Graphics::Panel::png('Bio::Graphics::Panel=HASH(0x1b1f6b0)') called at test.cgi line 37
Debugged program terminated.  Use q to quit or R to restart,
  use o inhibit_exit to avoid stopping after program termination,
  h q, h R or h o to get additional info.

#####################################################

Is it because of some incompatibility between version of bioperl and bio::Graphics or some thing else?

Thanks,
Mustafa.

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