[Bioperl-l] help with PHRAP assembly & Bio::Graphics

[Mariano Latorre A]

Hi!

I'm developing a bioperl cgi to show a png PHRAP assembly using
Bio::Graphics + perl cgi.

The problem is that the Contig deffines the zero position and usually
the alignment ESTs are located before the contig. This implies I need to
use negative positions...but Bio::graphics doesn't allow to use negative
positions...it just cuts them off.

PD: I paste my source code.
-- 
Mariano Latorre A <malatorr at genoma.ciencias.uchile.cl>
Universidad de Chile

######################################################################################
#THE CGI "render.pl"

#!/usr/bin/perl


use CGI;
use lib "$ENV{HOME}/projects/bioperl-live";
use Bio::Graphics;
use Bio::SeqFeature::Generic;

my $form = new CGI;
print "Content-type: image/png\n\n";

my $panel = Bio::Graphics::Panel->new(-length => 2000,-width  => 1800, -
pad_left => 10, -pad_right => 10,);

my $full_length = Bio::SeqFeature::Generic->new(-start=>$form->param
("start"),-end=>$form->param("end"));

$panel->add_track($full_length,
                  -glyph   => 'arrow',
                  -tick    => 2,
                  -fgcolor => 'black',
                  -double  => 1,
                 );

my $track = $panel->add_track(-glyph => 'graded_segments',
                              -label  => 1,
                              -bgcolor => 'blue',
                              -min_score => -200,
                              -max_score => 1000);


for($i=1;defined($form->param("est$i"));$i++){
  my($name,$score,$start,$end) = split /\@/,$form->param("est$i");
  my $feature = Bio::SeqFeature::Generic->new(-display_name=>$name,
            -score=>$score,
            -start=>$start,
            -end=>$end);
  $track->add_feature($feature);
}
print $panel->png;


######################################################################################
# The Url to call the CGI
render.pl?
est1=hola at 300@-200 at 367@&est2=chau at 50@300 at 600@&est3=nada at 50@310 at 25@&start=1&end=800

######################################################################################