[Bioperl-l] Boxes and features...

[Lincoln Stein]

The boxes() call gives you back what you put in via add_track() and 
add_feature().  So in this case you're adding a new Bio::SeqFeature::Generic 
for each blast hit, and each one has the tags "name" and "description".  You 
should get the same exact objects out when you call boxes().

Lincoln


On Thursday 27 February 2003 10:27 am, William Boileau wrote:
> I don't understand much how it all works :\
> what is the kind of feature we get with the boxes ?
> I would say Bio::SeqFeature::Generic, but I am not sure... and what are
> the tags we can get with the features ? can they be entered manually
> ?Because in the code below, when i try to list the tags in the feature of a
> box, they're empty... And to be honest, this is not exactly what i expected
> :DIf you have any idea, it would be really helpful! thanks !
>
> William Boileau
>
>
> ----------
> $searchio = new Bio::SearchIO ('-format' => 'blast',
> 			       '-file' => "blast_will.out");
>
> $result = $searchio->next_result;
>
> #Create a panel object
> my $panel = Bio::Graphics::Panel->new( -length =>$result->query_length,
> 				       -width => 1000,
> 				       -pad_left => 10,
> 				       -pad_right => 10,
> 				     );
>
> my $full_length = Bio::SeqFeature::Generic->new(-start => 1,
> 						-end => $result->query_length,
> 						-seq_id=> $result->query_name
> 					       );
> $panel->add_track($full_length,
> 		  -glyph   => 'arrow',
> 		  -tick    => 2,
> 		  -fgcolor => 'black',
> 		  -double  => 1,
> 		  -label   => 1,
> 		 );
>
> my $track = $panel->add_track(-glyph        => 'graded_segments',
> 			      -label        => 1,
> 			      -connector    => 'dashed',
> 			      -bgcolor      => 'blue',
> 			      -font2color   => 'red',
> 			      -sort_order   => 'high_score',
> 			      -box_subparts => 1,
> 			      -description  => sub {
> 				my $feature = shift;
> 				return unless $feature->has_tag('desription');
> 				my ($description) = $feature->each_tag_value('description');
> 				my $score = $feature->score;
> 				"$description, score=$score";
>                                  }
> 			     );
>
> while( my $hit = $result->next_hit ) {
>   next unless $hit->significance < '1e-20';
>   my $feature = Bio::SeqFeature::Generic->new(-score  => $hit->raw_score,
> 					      -seq_id => $hit->name,
> 					      -tag    => {
> 							  description => $hit->description,
> 							  name => $hit_name
> 							 },
> 					     );
>   while( my $hsp = $hit->next_hsp ) {
>     $feature->add_sub_SeqFeature($hsp,'EXPAND');
>   }
>
>   $track->add_feature($feature);
> }
>
> my @boxes = $panel->boxes;
> foreach ( $panel->boxes() ) {
>    my $feature_box = $_->[0];
>    my $coords  = join( ',', @{$_}[1..4] );
>
>    my @tags = $feature_box->get_all_tags();
>    foreach $x (@tags) {
>      print $x;
>    }
> }
>
>
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================