[Bioperl-l] Bio::TreeIO

[Rob Edwards]

On Tuesday, December 16, 2003, at 09:28  AM, Iain Wallace wrote:

> Hi all,
>
> I am trying to use the Bio::TreeIO module to split my sequences into 
> two
> groups.
>
> My problem is that I want these two groups to contain as many sequences
> as possible. At the moment I am using NJplot to define an outgroup, so
> that the tree is as evenly split as i can make it.
>
> I am wondering if any one knows an easier way to do this.....?
>
> Any help would be great
>
> Thanks
>
> Iain

Here is one (totally inelegant) way to get parts of a tree.

The two attached scripts work together. The first adds CountXXX (where 
XXX is the number of the node) to each node as an id on internal nodes 
and writes out the tree. You can then look at the tree (e.g. using atv 
or treeview) and decide which node you want to cut the tree at.

The second script takes the tree file and the node id (CountXXX) and 
just writes out that part of the tree.

Its not exactly what you want (I don't think) but it may put you on the 
right track.


add_tree_node_counts.pl
--------begin
#!/usr/bin/perl -w

# add node counts to a tree

use strict;
use Bio::TreeIO;

my $file=shift || die "tree file?";
my $tio=Bio::TreeIO->new(-file=>$file, -format=>'newick');
my $tout=Bio::TreeIO->new(-file=>">$file.nwk", -format=>'newick');
my $count=1;
while (my $tree=$tio->next_tree) {
  foreach my $node ($tree->get_nodes) {
    $node->id("Count$count") unless ($node->id);
    $count++;
  }
  $tout->write_tree($tree);
}
-------end


trim_tree.pl
-------begin
#!/usr/bin/perl -w

# trim a tree to a selected node

use strict;
use Bio::TreeIO;
use Bio::Tree::Tree;

my ($file, $nodeid)=@ARGV;
unless ($file && $nodeid) {die "$0 <treefile> <node id>"}

my $tio=Bio::TreeIO->new(-file=>$file, -format=>'newick');
my $tout=Bio::TreeIO->new(-file=>">$nodeid.nwk", -format=>'newick');
while (my $tree=$tio->next_tree) {
  print "Whole tree total length is ", $tree->total_branch_length, "\n";
  foreach my $node ($tree->get_nodes) {
   my $val=$node->id;
     if ($val && $val eq $nodeid) {
    my $newtree=Bio::Tree::Tree->new(-root=>$node);
    print "Trimmed total length is ", $newtree->total_branch_length, 
"\n";
    $tout->write_tree($newtree);
   }
  }
}
------end