[Bioperl-l] reading and writing tree

Peter Menzel pmenzel at googlemail.com
Mon Mar 30 09:56:02 EDT 2009


using the TreeIO class, I try to read a tree from a newick file,
delete some nodes, and write the tree using write_tree().
Besides that I cannot write to files, that don't exist already, it's
also not possible to write to existing files.
The following error message is written:

Filehandle GEN1 opened only for input at
/usr/share/perl5/Bio/Root/IO.pm line 421.

So apparently somehow a file handle is associated with the tree, since
different TreeIO objects are used.
Is there a workaround for this problem?

The actual code I run:

#!/usr/bin/perl -w

use strict;
use Bio::TreeIO;

my $filename = shift @ARGV;

# parse in newick/new hampshire format
my $input = new Bio::TreeIO(-file   => $filename,
                            -format => "newick");
my $tree = $input->next_tree;

foreach my $nodename (@ARGV) {
	my @nodes = $tree->find_node(-id => $nodename);
	if(@nodes > 0) {
		foreach my $n (@nodes) {

#write tree to new file
my $output = new Bio::TreeIO(-file => $filename.".new", -format => "newick");

kind regards, Peter

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