Capture Output to stream and store as a string variable

Question

Although this question relates to 'BioPerl', the question, I believe, is probably more general than that.

Basically I have produced a Bio::Tree::TreeI object and I am trying to convert that into a string variable.

The only way I can come close to converting that to a string variable is to write that tree to a stream using:

# a $tree = Bio::Tree::TreeI->new() (which I know is an actual tree as it prints to the terminal console)

my $treeOut = Bio::TreeIO->new(-format => 'newick')
$treeOut->write_tree($tree)

The output of ->write_tree is "Writes a tree onto the stream" but how do I capture that in a string variable as I can't find another way of returning a string from any of the functions in Bio::TreeIO

Answer 1

There is an easier way to accomplish the same goal by setting the file handle for BioPerl objects, and I think it is less of a hack. Here is an example:

#!/usr/bin/env perl

use strict;
use warnings;
use Bio::TreeIO;

my $treeio  = Bio::TreeIO->new(-format => 'newick', -fh => \*DATA);
my $treeout = Bio::TreeIO->new(-format => 'newick', -fh => \*STDOUT);

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

__DATA__
(A:9.70,(B:8.234,(C:7.932,(D:6.321,((E:2.342,F:2.321):4.231,((((G:4.561,H:3.721):3.9623,
I:3.645):2.341,J:4.893):4.671)):0.234):0.567):0.673):0.456);

Running this script prints the newick string to your terminal, as you would expect. If you use Bio::Phylo (which I recommend), there is a to_string method (IIRC), so you don't have to create an object just to print your trees, you can just do say $tree->to_string.