[Bioperl-l] coloring of HSPs in blast panel

Bernd Web bernd.web at gmail.com
Wed Nov 21 11:42:40 EST 2007


Hi Russell,

I came across your question. At first I thought all was well on my
system, but indeed I also have these colouring problems.
I noted that scrore in the bgcolor callback gets a different value!
Printing score during hit parsing($hit->raw_score) gives the same
score as -description
my $score = $feature->score; However, printing score in the bgcolor
sub gives 2573!
All scores in the bgcolor routine all different and higher than the
real scores. Were you able to solve this colouring issue?

Regards,
Bernd

> Hi all,
> I'm using a modified version of Lincoln's tutorial
> (http://www.bioperl.org/wiki/HOWTO:Graphics#Parsing_Real_BLAST_Output)
> 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
> $feature->has_tag('description');
>                                 my ($description) =
> $feature->each_tag_value('description');
>                                 my $score = $feature->score;
>                                 "$description, score=$score";
>                                },
>                              );
> ------------------------------------------------------------------------
> ---------
>
>
> Thanx,
>
> Russell Smithies
>
>
>
>
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