[Bioperl-l] Problem with Bio::PopGen::Individual

Jason Stajich jason at bioperl.org
Fri Jul 13 16:17:31 EDT 2007

Hi Sheri -

Shoot - that was my fault - bug in the code where I was only using  
"Person" not Individuals for the code when I was testing.

I've commited a bugfix to CVS - do you need me to send you the  
updated file or are you comfortable grabbing the code from CVS or  

This is the change - you may have a different version of BioPerl than  
what is in CVS so you may have to make the changes on line 260 rather  
than 282 -- or you can upgrade to latest code via CVS (although this  
is probably harder for you since you've got stuff installed in /usr/ 

RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/ 
retrieving revision 1.22
diff -r1.22 Population.pm
<       unshift @tosplice, $i if( $namehash{$ind->person_id} );
 >       unshift @tosplice, $i if( $namehash{$ind->unique_id} );

On Jul 13, 2007, at 2:42 PM, Sheri Simmons wrote:

> Hi,
> I have a collection of sequencing reads aligned with a consensus  
> sequence that
> I input into a Bio::PopGen::Population object in order to calculate  
> allele
> frequencies. The consensus sequence is included to force clustalw  
> to give a
> better alignment. However,  I need to remove the consensus sequence  
> before
> calculating allele frequencies in the individual reads. I'm having  
> trouble
> with this part of it. I get the following error message:
> "Can't locate object method "person_id" via package  
> "Bio::PopGen::Individual" 		
> at /usr/share/perl5/Bio/PopGen/Population.pm line 260, <GEN0> line  
> 49."
> Here is the code snippet producing the error. $pop is a
> Bio::PopGen::Population object.
> 	my @consensus = "gene_consensus";
> 	$pop->remove_Individuals(@consensus);
> I also tried:
> 	my @consensus = $pop->get_Individuals(-unique_id =>  
> "gene_consensus");
> 	$pop->remove_Individuals(@consensus);
> which produced the same error. Can anyone send me in the right  
> direction? I
> suspect this is a simple problem.
> Sheri
> -- 
> Sheri Simmons
> Department of Earth and Planetary Sciences
> University of California, Berkeley
> Berkeley, CA 94720-4767
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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Jason Stajich
jason at bioperl.org

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