[Bioperl-l] Bio::TreeIO -> Reconstructing Newick

[Joseph Ryan]

I am trying to read in a Newick Treefile, make some adjustments to the
bootstrap values, and then print back out a treefile.  Reading in the treefile
is a breeze with the Bio::TreeIO module.

    my $treeio = new Bio::TreeIO('-format' => 'newick',
                                 '-file'   => 'treefile.consense');

Adjusting the bootstrap values should be fairly straight forward, but I have
come across a snag in trying to generate an updated newick treefile.  I tried
to use the write_tree method from Bio::TreeIO:

    $treeio->write_tree($tree);

But I get the following error:

    Filehandle Symbol::GEN0 opened only for input at
/usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm

Is there an easy way to adjust the output stream?  Maybe to STDOUT?

Many thanks,
Joe Ryan
--


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