[Bioperl-l] Can Bio::Graphics render a muti_segments picture?

tongw tongw at genomics.org.cn
Tue May 13 12:00:20 EDT 2003


Hi, dear Lincoln:
       Thanks for your so quick response. It`s the problem of my English
expression about my previous question. My puzzle is:
    When your sequence is too long to be drawn in one line, can
Bio::Graphics help us to draw the long sequence in muti_parts, such as
drawing a 200k sequence in two parts, each is 100k. But not to say how
to draw  a muti_segments feature in a sequence.
       Because I want to write a script to draw the picture of genes`
annotation of small genomes by the Bio::Graphics module, which are too
long to display in one line. 
Kind Regards. 
                                                    Wei Tong


-----Original Message-----
From: Lincoln Stein [mailto:lstein at cshl.org] 
Sent: 2003Äê5ÔÂ12ÈÕ 21:54
To: tongw; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Can Bio::Graphics render a muti_segments
picture?


Here's an example of drawing a multi-segment object:

use strict;
use Bio::Graphics;
use Bio::SeqFeature::Generic;

my $Generic = 'Bio::SeqFeature::Generic';  # to reduce typing

# create a feature to use for the scale arrow
my $whole_region = $Generic->new(-start=>1,
-end=>10000,-seq_id=>'whole');

# create a multi-segment feature
my $blue1        =
$Generic->new(-start=>5000,-end=>9000,-seq_id=>'blue1');
$blue1->add_SeqFeature($Generic->new(-start=>5000,-end=>6000));
$blue1->add_SeqFeature($Generic->new(-start=>7000,-end=>7500));
$blue1->add_SeqFeature($Generic->new(-start=>8000,-end=>9000));

my $panel =
Bio::Graphics::Panel->new(-segment=>$whole_region,-width=>800);
$panel->add_track($whole_region,
                  -glyph  => 'arrow',
                  -double => 1,
                  -tick   => 2);

$panel->add_track($blue1,
                  -glyph   => 'segments',
                  -label   => 1,
                  -bgcolor => 'blue');

print $panel->png;

Best,

Lincoln



On Monday 12 May 2003 06:18 am, tongw wrote:
> Greeting all, especially the developers of Bioperl:
>     It`s my first time to locate the mail list of Bioperl, and I have 
> applied the Bioperl modules to sovle the problems in my research, 
> which is more comfotable than write the perl scripts, specially in the

> format changing and drawing the picture by GD module.
>   But I meet a question: I think the Bio::Graphics only draw the whole

> sequence in one segment. I want to know whether there is some methods 
> to render a muti_segments picture, and it is more necessary when the 
> sequence is very long. Kind Regards.
> Specially thank Lincoln, your howto docment about Graphics helps me to
> grasp the main usages in graphics module.
>
>                                                        Wei Tong
>
>
> ============================================
>
> Wei Tong
>
> Bioinformatics Department
> Beijing Genomics Institute/
> Genomics & Bioinformatics Center Chinese Academy of Science Beijing 
> Airport Industrial Zone B6 Beijing 101300, P.R. China
>
> Tel: 0086-10-80481833 (Office)
> Email : tongw at genomics.org.cn
> http://www.genomics.org.cn 
> ============================================
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org 
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-- 
Lincoln Stein
lstein at cshl.org
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)





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