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

[Jack Chen]

Hi Jason and all,

Have tried to use this module but got stuck the the message:
==============================================================
------------- EXCEPTION  -------------
MSG: Need a file or file handle!
STACK Bio::Matrix::PhylipDist::new
/usr/lib/perl5/site_perl/5.6.0/Bio/Matrix/PhylipDist.pm:116

==============================================================
My code is basically copied from the synopsis:

#!/usr/bin/perl -w
use strict; 
use lib "/a/blue2/home/BioPipe/bioperl-live/";

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

my $dist = Bio::Matrix::PhylipDist->new( -file => "outfine",
                                         -program =>"ProtDist");

#my $dist =
Bio::Matrix::PhylipDist->new(-fh=>"temp",-program=>"ProtDist");

#get specific entries 
my $distance_value = $dist->get_entry('CBG04330','T19D12.8');
#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;

print $distance_value, "\n";

Anything I am not aware of?

Thanks,

Jack

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|    o-o     Jack Chen, Stein Laboratory       |
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