[Bioperl-l] coloring of HSPs in blast panel

[Bernd Web]

Hi,

I now found that bgcolor is using a  $feature->score that is coming
directly from the blast report, it is not the bit score.
     -bgcolor     => sub {my $feature = shift;
                                  my $score = $feature->score;
				  print "$score\n"; }
always print the score, even if the score is not set in the
Bio::SeqFeature::Generic object.

-description callbacks are somehow using the score from the SeqFeature object.

Does anyone have an idea why?

Further is is possible to get the raw_score of a hit. $hit->raw_score
actually gets the bitscore (w/o decimal point).

Bernd

On Nov 21, 2007 5:42 PM, Bernd Web <bernd.web at gmail.com> wrote:
> 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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