[Bioperl-l] coloring of HSPs in blast panel

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Oct 2 21:05:25 EDT 2007

Hi all,
I'm using a modified version of Lincoln's tutorial
and I'm colouring the HSPs by setting the -bgcolor by score with a sub
to give a similar image to that from NCBI but for some reason, my
colours are coming out wrong (see attached example)
They seem to be off by one but I can't see why.

Any ideas?

I can't be certain but I think it's only started doing this since our
BLAST upgrade to 2.2.17 a few weeks ago.

Here's the colouring code:
my $track = $panel->add_track(
                              -glyph       => 'segments',
                              -label       => 1,
                              -connector   => 'dashed',
                              -bgcolor     => sub {
                                my $feature = shift;
                                my $score = $feature->score;
			return 'red'       if $score >= 200;
                                    return 'fuchsia' if $score >= 80;
                                    return 'lime'      if $score >= 50;
			return 'blue'      if $score >= 40;
                                    return 'black';
                              -font2color  => 'gray',
                              -sort_order  => 'high_score',
                              -description => sub {
                                my $feature = shift;
                                return unless
                                my ($description) =
                                my $score = $feature->score;
                                "$description, score=$score";


Russell Smithies

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