[Bioperl-l] Bio::Graphics::Panel can't locate object method 'start'...

[Lincoln Stein]

Hi Matt,

You and about a million other people have the same problem.  You can do one of 
two things:

	1) get the latest bioperl-live from CVS, where the problem is fixed 
transparently in Bio::Graphics::Panel

or

	2) make the following type of change in all your scripts:

OLD WAY:
 my $panel = Bio::Graphics::Panel->new(	-segment => $seq,
 							-key_style => 'between',
 							-pad_left  => 10,
 							-pad_right  => 10,
 							-width  => 800	);

NEW WAY:
 my $panel = Bio::Graphics::Panel->new( -length => $seq->length,
 							-key_style => 'between',
 							-pad_left  => 10,
 							-pad_right  => 10,
 							-width  => 800	);

Sorry about this, but Bioperl is large and amoeboid, and sometimes one 
pseudopodium doesn't know what the other is doing.

Lincoln

On Saturday 01 March 2003 12:08 pm, Matthew Vaughn wrote:
> Hello, all. First of all, let me introduce myself to the list as this
> is my first posting. I'm a postdoc in Rob Martienssen's lab at Cold
> Spring Harbor Lab where I work on a variety of plant genomic projects.
> I've been using BioPerl for about a year now and I find it absolutely
> invaluable.
>
> Here's my problem: I just took the plunge and upgraded my BioPerl
> installation from 1.02 to 1.2 and I've run into a problem with
> Bio::Graphics that has broken many of my scripts. Essentially, it looks
> like elements of Bio::Graphics are calling methods that Bio::Seq
> doesn't have any more. I've condensed the problem into the following
> code snippet. It should produce a blank panel image, but instead dies
> with an error 'Can't locate object method "start" via package
> "Bio::Seq" at /Library/Perl/Bio/Graphics/Panel.pm line 45, <DATA> line
> 141.'
>
> Am I doing something dunder-headed or is this a real bug?
>
> Thanks,
>
> Matt Vaughn
>
> #!/usr/bin/perl -w
>
> use Bio::Graphics;
> use Bio::SeqIO;
>
> my $io = Bio::SeqIO->new(-file=>'testing.fa');
> my $seq = $io->next_seq;
> my $panel = Bio::Graphics::Panel->new(	-segment => $seq,
> 							-key_style => 'between',
> 							-pad_left  => 10,
> 							-pad_right  => 10,
> 							-width  => 800	);
> my $gd = $panel->gd;
> print $gd->can('png') ? $gd->png : $gd->jpeg;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================