[Bioperl-l] newick to nexus

[Lewis Lukens]

Hi,

I am trying to convert tree files from newick to nexus format.  It 
seems that one can do this (using the example script from 
bio::factory::treefactoryI) but I have been unable to.

My the code is:

#!/usr/bin/perl
use Bio::TreeIO;
my $treeio= new Bio::TreeIO ('-format'=> 'newick', '-file'=>'bpoistree');
my $treeout= new Bio::TreeIO ('-format'=> 'nexus', '-file'=>'>outfile');

while(my $tree = $treeio->next_tree) {
       $treeout->write_tree($treeout);
}


The newick tree is fine, but the "nexus" module is missing, and I get 
the following error:

Bio::TreeIO: nexus cannot be found
Exception
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::TreeIO::nexus. Can't locate 
Bio/TreeIO/nexus.pm in @INC (@INC contains: 
/System/Library/Perl/darwin /System/Library/Perl /Library/Perl/darwin 
/Library/Perl /Library/Perl /Network/Library/Perl/darwin 
/Network/Library/Perl /Network/Library/Perl .) at 
/Library/Perl/Bio/Root/Root.pm line 407.

STACK Bio::Root::Root::_load_module /Library/Perl/Bio/Root/Root.pm:409
STACK (eval) /Library/Perl/Bio/TreeIO.pm:221
STACK Bio::TreeIO::_load_format_module /Library/Perl/Bio/TreeIO.pm:220
STACK Bio::TreeIO::new /Library/Perl/Bio/TreeIO.pm:121
STACK toplevel treeswitch.pl:4

Is there another way to do this in bioperl?

Thanks much,
Lewis

P.S. Please respond to the address above, as I am not a subscriber to 
the mailing list.
-- 
Lewis Lukens
Assistant Professor
Department of Plant Agriculture
Univ. of Guelph, Guelph, Ontario. N1G 2W1

Tel: (519) 824- 4120 ext 52304