[Bioperl-l] treeio->write_tree problem

Adam Witney awitney at sgul.ac.uk
Wed Oct 20 12:01:45 EDT 2010


you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):

my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
                           -format => "newick");

my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
                           -format => "newick");

while( my $tree = $treeio->next_tree ) {
	$treeio_out->write_tree($tree);
	print Dumper($tree);
}



On 20 Oct 2010, at 16:27, Jim Hu wrote:

> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
> 
> Jim
> 
> use Data::Dumper;
> use Bio::TreeIO;
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                            -format => "newick");
> while( my $tree = $treeio->next_tree ) {
> 	$treeio->write_tree($tree);
> 	print Dumper($tree);
> 
> }
> 
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
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