[Bioperl-l] How can I get add_sub_SeqFeature to work as I want?

[Allen Day]

someone correct me if i'm wrong, but i think you need to add all the
features for a track at once.  maybe you should load this file into a 
database (even SQLite) so you don't have to keep track of the 
previous_row/next_row-ness of the text file.

-allen

On Wed, 24 Nov 2004, Marcus Claesson wrote:

> Hi!
> 
> I've had a problem some time with getting the add_sub_SeqFeature to work
> for my own parsed blast data. Last time I posted it to the list nobody
> was be able to help me, but I have now simplified the problem a bit.
> 
> I have blast parsed data like this in a text file (the columns are
> sbj_count,hsp_count,score,query_begin,query_end,strand),(I left out
> sbj_name for simplicity):
> 1	1	445	1148	375	-1
> 1	2	341	1717	1151	-1
> 2	1	364	1148	378	-1
> 2	2	344	1690	1151	-1
> 3	1	283	1145	381	-1
> 3	2	233	1714	1151	-1
> 4	1	182	1154	375	-1
> 4	2	124	1702	1160	-1
> 
> The only way I know the hit has more than one hsp is if the next line
> has the same sbj_count. Based on this I'd like to construct a Graphics
> Panel as an graphical overview of the blast hits. Below is the script
> that shows every hsp as separate hits (I want hsps belonging to the same
> hit on one line):
> 
> #!/usr/bin/perl
> use Bio::Graphics;
> use Bio::SeqFeature::Generic;
> my $panel = Bio::Graphics::Panel->new(-length    => 2000,
>                                        -width     => 500,
>                                        -pad_left  => 10,
>                                        -pad_right => 10);
> 
> my $track = $panel->add_track(-glyph        => 'graded_segments',
>                               -label        => 1,
> 			      -strand_arrow => 1,
>                               -connector    => 'dashed',
>                               -bgcolor      => 'blue',
>                               -font2color   => 'red',
>                               -sort_order   => 'score',
>                               -description  => sub {
>                                    my $feature = shift;
>                                    my ($score) = $feature->score;
>                                    "Score=$score"});
> 
> $old_sbj_count = 0;
> while (<>) {
>     ($sbj_count,$hsp_count,$score,$qbegin,$qend,$strand) = split;
>     my $feature = Bio::SeqFeature::Generic->new(-start   => $qbegin,
> 						-end     => $qend,
> 						-strand  => $strand,
> 						-score   => $score);
>     if ($old_sbj_count eq $sbj_count) {
> 	my $subfeature = Bio::SeqFeature::Generic->new(
>                                                    -start => $qbegin,
> 						   -end   => $qend,
> 						   -strand=> $strand,
> 						   -score => $score);
> 	$feature->add_sub_SeqFeature($subfeature,"EXPAND");
>     }
>     $old_sbj_count = $sbj_count;
>     $track->add_feature($feature);
> }
> print $panel->png;
> 
> 
> I would be extremely grateful for any help on this since I've been
> struggling for a long time...
> 
> Best regards,
> Marcus
> 
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