[Bioperl-l] How to 'force' Bio::Graphics to draw image according to input file ?

Shameer Khadar shameer at ncbs.res.in
Wed Aug 22 15:45:42 EDT 2007


Dear All,

Is there any option in Bio::Graphics to draw image based on the hits as
explained in the hits file.

For example I am using an input file:
# hit   score   start   end
Query   0       1       101
Sequence_Segment_1      0       1       101
PD:LRR_1|CS:AAC34139        0.16        1        23
PD:LRR_1|CS:AAC34139        3.6        1        22
PD:LRR_1|CS:AAC34139        1.8        1        22
PD:LRR_1|CS:AAC34139        1.3        1        22
PD:LRR_1|CS:XP_640228        2.5        2        23
..... Cropped
PD:LRR_1|CS:NP_611007        55        3        23
PD:LRR_1|CS:NP_611007        3.7        3        24
PD:LRR_1|CS:NP_611007        4.5        3        24
PD:LRR_1|CS:NP_611007        0.71        3        24
If you look at the image, you can see that, its all jumbled up and it
doesnt make any sense in the first look. I am looking for an option to
draw each of the  glyph one by one (say \n), rather that accomodating it
internally by the Bio::Graphics.

PS. Image is attached with this mail.
I am using  Dr. L. Stein's example :

use strict;
use Bio::Graphics;
use Bio::SeqFeature::Generic;
my $panel = Bio::Graphics::Panel->new(-length => 700,
                                      -width  => 800,
                                      -pad_left => 10,
                                      -pad_right => 10,
                                     );

my $full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>700);
$panel->add_track($full_length,
                  -glyph   => 'arrow',
                  -tick    => 2,
                  -fgcolor => 'black',
                  -double  => 1,
                 );

my $track = $panel->add_track(
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