[Bioperl-l] Graphics:Panel /SeqFeature::Generic

[Lincoln Stein]

Hi Dan,

Try changing the "generic" glyph to "segments."  The first glyph doesn't know 
how to deal with subparts (such as HSPs), the second does.

Lincoln

On Monday 17 November 2003 05:06 am, Daniel Lang wrote:
> Hi,
> I want to generate overview graphics from BLAST reports, where the hits
> are sorted and colored (>1e-10 -->green, ...)according their evalues...
>
> So I thought, I could solve this using a callback function for the
> bgcolor and using the 'low_score' sort_order, but when applied to a
> BLAST report, it results in sorted but only red hits?
> I also tried introducing the evalues as additional tags like done with
> 'bits' or 'range', but when testing for this tag in the callback
> (has_tag) its not available?
> So I wander if the function is envoked for each hit in the while loop?
>
> Here the code sniplet:
>
> my $track = $panel->add_track(-glyph       => 'generic',
>                                  -label       => 1,
>                                  -connector   => 'dashed',
> 				-height      => 5,
>                                  -bgcolor     =>  sub {
> 						    my $feature = shift;
> 						    my $evalue = $feature->score;
> 						    if ($evalue < 1e-10) {return 'green';}
> 						    else {return 'red';}}
> 						    ,
> 				-fontcolor   => 'green',
>                                  -font2color  => 'red',
>                                  -sort_order  => 'low_score',
> 				-min_score => '1e-1000',
> 				-max_score => '10000',
>                                  -description => sub {
>                                    my $feature = shift;
>                                    return unless $feature->has_tag('bits');
>                                    my ($description) =
> $feature->each_tag_value('bits');
>                                    my $score = $feature->score;
>                                    my ($range) =
> $feature->each_tag_value('range');
> 				  "Score=$description bits, E-value=$score, $range";
>                                   });
>
>      while( my $hit = $result->next_hit ) {
> 	my $evalue = $hit->significance;
> 	my $feature = Bio::SeqFeature::Generic->new(-score   => $evalue,
> 						    -display_name => $hit->name,
> 						    -tag     => { 'bits' => $hit->bits,
> 								  'range' => "from ". $hit->start('query') . " to " .
> $hit->end('query'),
> 								  },
> 						    );
> 	while( my $hsp = $hit->next_hsp ) {
> 	   $feature->add_sub_SeqFeature($hsp,'EXPAND');
> 	 }
> 	$track->add_feature($feature);
>    }
>
> Thanks in advance,
> Daniel
>
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================