[Bioperl-l] drawing a quality trace on a panel?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Oct 14 23:28:23 EDT 2008


Hi all,
I'm writing a contig viewer and want to add a trace of quality trace
data.
I can get the values OK but how do I draw these on a panel with the
xyplot glyph?
Any ideas?


Here's some example code:
(sorry if Outlook will screws up the formatting)

=====================================
my $parser = new Bio::Assembly::IO(-file   => $infile ,-format => "ace")
or die $!;

# just work on the first contig
my ($contig) = $parser->next_assembly->all_contigs;

my $consensus = $contig->get_consensus_sequence();

my @quality_values  = @{$contig->get_consensus_quality()->qual()};

#create panel
my $panel = Bio::Graphics::Panel->new(
	                              	-length   => $consensus->length,
	                              	-width    => gdSmallFont->width
* 1.5 * $consensus->length,
				-bgcolor  => 'white',
				-grid => 1,
				-pad_left=> 20,
				-pad_right=> 20,
				);

# add a scale
$panel->add_track('arrow' => Bio::Graphics::Feature->new(
						      	-start =>
$consensus->start,
						    	-end   =>
$consensus->end ),
							-bump   => 0,
							-double => 1,
							-tick   => 2,
						      	);

my $consensus_feature = Bio::SeqFeature::Generic->new(
							-start =>
$consensus->start,
							-end   =>
$consensus->end,
							-strand=>
$consensus->strand,
							-display_name =>
$consensus->display_name,
							);

my $consensus_seq = Bio::PrimarySeq->new( -seq => $consensus->seq);
$consensus_feature->attach_seq($consensus_seq);
$panel->add_track( $consensus_feature,
					-glyph => 'segments' ,
					-height => 10,
					-label  => 1, 
					-draw_dna  => 1,
					-bgcolor  => "white", 
					-fgcolor => "silver"
					);

# somehow get the array of quality_values into an xyplot?


#other code to draw rest of the reads

# output
print $panel->png;

=======================================
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