[Bioperl-l] Please help with Bio::Graphics

Lucas Quincy Ton lton at nd.edu
Mon Feb 3 17:53:38 EST 2003


Dear all,
     I have recently started using the Bio::Graphics module to render a png 
picture from an embl-formatted file.  Everything so far looks fine but when I 
coded the 'dna' glyph to render GC-content plot, I get the plot but with just 
a straight line in the middle (50%) from lelf to right.  Would someone please 
gear me to the right direction?  My code is as follow:

#I create a SeqFeature::Generic object
my $gcfeature = Bio::SeqFeature::Generic->new(-start=>1,
					      -end=>$seq->length,);
#here I attach the whole DNA sequence referenced by $seq to the feature
#I do this because I read perldoc on dna.pm which specified that "the feature
#must return a DNA sequence string in response to the dna() method -- so I 
made
#my best guess as to its meaning
$gcfeature->attach_seq($seq);
#now I create a track for GC content
$panel->add_track($gcfeature,
     -glyph	=> 'dna',
     -fgcolor => 'black',
     -height => 100,
     -bgcolor => 'red',
     -do_gc	=> 'true',
     -gc_bins => 10,
     -axis_color=> 'blue',
     -strand => 'forward',);

Any response will be greatly appreciated.
Lucas Ton.



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