[Bioperl-l] Bio::Graphics

[Wes Barris]

Laurence Amilhat wrote:

> Hi,
> 
> I try to learn how to use the module Bio::Graphics.
> I found he How To from Lincoln Stein on the web. I try to practice with
> the examples, it's working except for the labels of the features that 
> don't appear on my figure.
> Does anybody ever use this module?

Hi Laurence,

I have not been able to get this function working either.  I am experiencing
the exact same problem as you.  I have tried this on two separate computers
where bioperl was installed by two different people.  Both are Redhat systems.
One is running bioperl-1.2.1, the other is running bioperl-1.2.2.  In both
cases the labels are silently omitted.

The example that I was trying is the first one on this page:

	http://bioperl.org/HOWTOs/html/Graphics-HOWTO.html

It is virtually the same as your example with one small difference.  You
code includes this line:

my $feature = Bio::SeqFeature::Generic->new(-display_name=>$name,-score=>$score,

The example from the URL above uses a slight variation:

my $feature = Bio::SeqFeature::Generic->new(-seq_id=>$name,-score=>$score,

I have tried both versions.  Neither of them produced a label in the
resulting png file.  I don't know what the significance of the two different
attributes is.  I can read the words of the documentation, but it didn't
explain the difference of the two or if they were somehow related.

Obviously, there is a bug somewhere in bioperl or in the provided examples
(or in the provided installation instructions).  Either that, or we have
both made the exact same error in doing something.  I just don't know what.

I have posted a question about this exact same anomaly to this mailing list
but have not received any suggestions yet.  Perhaps this module is not too
heavily used.

> 
> This is the example:
> #!/usr/local/public/bin/perl
> 
> use strict;
> use lib 
> '/homej/bioinf/lamilhat/PERL_MODULE/lib/perl5/site_perl/5.005/BIOPERL/li
> b/site_perl/5.6.1/';
> use Bio::Graphics;
> use Bio::SeqFeature::Generic;
> 
> my $panel= Bio::Graphics::Panel->new(-length =>1000,-width =>800);
> my $track=$panel->add_track(-glyph =>'generic',-label =>1);
> 
> 
> while (<>)
> {
>         chomp;
>         next if /^\#/;
>         my ($name,$score,$start,$end)=split /\t+/;
>         print STDERR "$name\n";
>         my $feature= 
> Bio::SeqFeature::Generic->new(-display_name=>$name,-score=>$score,-start
> =>$start,-end=>$end);
>         $track->add_feature($feature);
> }
> 
> print $panel->png;
> 
> 
> And this is the Data to parse with the example:
> #hit    score   start   end
> truc1   381     2       200
> truc2   210     2       210
> truc3   800     2       200
> truc4   1000    380     921
> truc5   812     402     972
> truc6   1200    400     970
> bum     400     300     620
> pres1   127     310     700
> 
> 
> Thanks,
> 
> Laurence.
> 
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-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au