[Bioperl-l] chromatogram
Lee Katz
lskatz at gatech.edu
Fri Jul 3 22:08:43 UTC 2009
Thank you Scott. I know that this message is really late, but I got really side
tracked and want to follow through with this. My code so far is a mutt between
everything I found online. It only produces a generic track though; however, I
want to produce a chromatogram image, as shown on the gbrowse tutorial I found
at http://wheat.pw.usda.gov/gbrowse/tutorial/tutorial.html (section 15:
Displaying Trace Data, where a semantic zoom is shown). Can you guys help me
finish it off? Thanks.
use Bio::Graphics;
use Bio::Seq;
use Bio::SeqFeature::Generic;
my @scfFile=qw(1.scf 2.scf);
my $bsg = 'Bio::SeqFeature::Generic';
my $seq = Bio::Seq->new(-length=>900);
my $whole = $bsg->new(-display_name => 'Clone82',
-start => 1,
-end => $seq->length);
my $trace1 = $bsg->new(-start => 1,
-end => 500,
-display_name => 'Trace',
-tag=>{
trace=>"$scfFile[0]"
}
);
my $panel = Bio::Graphics::Panel->new(-length => $seq->length,
-width => 800,
-truecolor => 1,
-key_style => 'between',
-pad_left => 10,
-pad_right => 10,
);
$panel->add_track($whole,
-glyph => 'arrow',
-double => 1,
-tick => 2,
-label => 1,
);
$panel->add_track([$trace1],
-feature=>'read',
-strand_arrow=>1,
-glyph => 'trace',
-a_color=>'green',
-c_color=>'blue',
-g_color=>'black',
-t_color=>'red',
-trace_height=>80,
-description=>1,
-label => 1,
-key => 'Traces');
binmode STDOUT;
print $panel->png;
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