[Bioperl-l] adding HSP information to BLAST output graphic (Bio::Graphics)

Adam Witney awitney at sgul.ac.uk
Wed Aug 27 12:21:12 EDT 2008


after some digging around myself, this seems to do the trick, although  
i don't know if it will always work, as i am having to add a separate  
sort function.

On 21 Aug 2008, at 15:41, Adam Witney wrote:

>
> Hi,
>
> I am going through the Bio::Graphics HOWTO on the wiki.
>
> Looking at render_blast4.pl, the description text describes the  
> whole hit and is set for the whole track, but i would like to be  
> able to add HSP information such as the identity matches onto the  
> picture, this is stored in the $hsp object. How would i go about  
> adding that to the picture?
>
> the relevant piece of code is:
>
>      my $track = $panel->add_track(
>                                    -glyph       => 'graded_segments',
>                                    -label       => 1,
>                                    -connector   => 'dashed',
>                                    -bgcolor     => 'blue',
>                                    -font2color  => 'red',
>                                    -sort_order  => 'high_score',

                                     -part_labels => sub {
                                       my ($feature,undef,$partno) = @_;
                                       my @features =  
sort_features($feature->get_SeqFeatures());
                                       return $features[$partno]- 
 >num_identical.'/'.$features[$partno]->length.' (score='. 
$features[$partno]->score.')' if $features[$partno];
                                      },

>                                    -description => sub {
>                                      my $feature = shift;
>                                      return unless $feature- 
> >has_tag('description');
>                                      my ($description) = $feature- 
> >each_tag_value('description');
>                                      my $score = $feature->score;
>                                      "$description, score=$score";
>                          #            "score=$score";
>                                     },
>                                   );


sub sort_features {
   my @array = @_;

   if(@array < 2){return @array}

   my @sorted = sort {$a->start <=> $b->start} @array;

   return @sorted;
}


is this the best way to achieve this?

thanks

adam



More information about the Bioperl-l mailing list