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

Sheri Simmons sheris at eps.berkeley.edu
Fri Jul 13 14:42:32 EDT 2007


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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