[Bioperl-l] Using Bio::Matrix::PhylipDist

Iain Wallace iain.wallace at ucd.ie
Mon Feb 28 06:23:58 EST 2005

Hi all,

I hope someone can help me.  I am trying to  read in a distance matrix 
using  Bio::Matrix::PhylipDist so that I can extract a subset of the 
matrix. However I am having some trouble reading in the Matrix.
I have tried a few different matrices so I don't think that is the 
problem. If any one has an idea on what I am doing wrong that would be great

I have tried a few of the examples I found, but cann't seem to get them 
to work. It seems to be falling over at the $parser->next_matrix phase.

---Some of the examples I tried (from the module documentation) ----
from Bio::Matrix::IO::phylip
use Bio::Matrix::IO;
  my $parser = new Bio::Matrix::IO(-format   => 'phylip'
                                   -file     => 't/data/phylipdist.out');
  my $matrix = $parser->next_matrix;

Error: Can't use an undefined value as an ARRAY reference at (full 
path)/Bio/Matrix/Generic.pm line 731

from Bio::Matrix::PhylipDist

use Bio::Tools::Phylo::Phylip::ProtDist;

  my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new(
  #get specific entries
  my $distance_value = $dist->get_entry('ALPHA','BETA');
  my @columns        = $dist->get_column('ALPHA');
  my @rows           = $dist->get_row('BETA');
  my @diagonal       = $dist->get_diagonal();

  #print the matrix in phylip numerical format
  print $dist->print_matrix;

Error: Cann't locate object method "get_entry" via package.

Then I modified the code, after looking at the  ProtDist.pm file
my $dist = $parser->next_matrix or die "could not parse matrix";
My script then dies at this point, not being able to parse the matrix.



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