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

[Daniel Lang]

Hi again,
I tested it also on the command line using an additional tag called 
'sig' but the problem is the same:
------------- EXCEPTION  -------------
MSG: asking for tag value that does not exist sig
STACK Bio::SeqFeature::Generic::get_tag_values 
/usr/lib/perl5/site_perl/5.6.1/Bio/SeqFeature/Generic.pm:504
STACK main::__ANON__ ./htmlresult1.pl:105
STACK (eval) 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph/Factory.pm:394
STACK Bio::Graphics::Glyph::Factory::option 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph/Factory.pm:394
STACK Bio::Graphics::Glyph::option 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph.pm:321
STACK Bio::Graphics::Glyph::bgcolor 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph.pm:386
STACK Bio::Graphics::Glyph::filled_box 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph.pm:830
STACK Bio::Graphics::Glyph::draw_component 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph.pm:959
STACK Bio::Graphics::Glyph::segments::draw_component 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph/segments.pm:63
STACK Bio::Graphics::Glyph::draw 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph.pm:650
STACK Bio::Graphics::Glyph::generic::draw 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph/generic.pm:107
STACK Bio::Graphics::Glyph::draw 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph.pm:642
STACK Bio::Graphics::Glyph::generic::draw 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph/generic.pm:107
STACK Bio::Graphics::Glyph::track::draw 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Glyph/track.pm:21
STACK Bio::Graphics::Panel::gd 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Panel.pm:461
STACK Bio::Graphics::Panel::png 
/usr/lib/perl5/site_perl/5.6.1/Bio/Graphics/Panel.pm:781
STACK main::create_overview ./htmlresult1.pl:147
STACK toplevel ./htmlresult1.pl:20

--------------------------------------
Any hints?

Daniel


Lincoln Stein wrote:

> 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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> 
>