in reply to how to output the final Tree into a file?

You can open a file for writing and pass the file handle into Bio::TreeIO->new.

...
my $outfile = '/path/to/file/to/create';
open my $fh, '>', $outfile or die "Cannot create $outfile, $!\n";
my $treeout = Bio::TreeIO->new(-format => 'newick', -fh => $fh);
...

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Alternately, you can simply pass a filename to Bio::TreeIO->new.

...
my $outfile = '/path/to/file/to/create';
my $treeout = Bio::TreeIO->new(-format => 'newick', -file => ">$outfil
+e");
...

[download]

Replies are listed 'Best First'.
Re^2: how to output the final Tree into a file?
by 1nickt (Canon) on Mar 16, 2016 at 00:40 UTC

    Hmm, I've not used it myself, but the docs seemed pretty clear that the file/filehandle is for reading, and that Bio::TreeIO doesn't have a print method, but relies on you to print the contents of the tree. From the DESCRIPTION: 

    This is the driver module for Tree reading from data streams and flatf
+iles. This is intended to be able to create Bio::Tree::TreeI objects.

    [download]
    and the SYNOPSIS: 
    {
      use Bio::TreeIO;
      my $treeio = Bio::TreeIO->new(-format => 'newick',
                                    -file   => 'globin.dnd');
      while( my $tree = $treeio->next_tree ) {
                print "Tree is ", $tree->number_nodes, "\n";
      }
  }

    [download]
    In this case the OP has created his tree with Bio::TreeIO and it's held in $treeout.

    The way forward always starts with a minimal test.
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Re^2: how to output the final Tree into a file?
by dimitris852 (Acolyte) on Mar 15, 2016 at 23:46 UTC

    I did that

    my $outfile = 'C:\Users\Ioulia\Desktop\outree.tre';
my $treeout = Bio::TreeIO->new(-format => 'newick', -file => ">$outfil
+e");

    [download]

    But I get this: "my" variable $treeout masks earlier declaration in same scope at....line 50.

    Then I can normaly run the script but an empty file outree.tre is created.

    please excuse me but I m really new and it takes me a long time to understand many things

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[d/l]

      please excuse me but I m really new and it takes me a long time to understand many things

      :) fragments which don't reproduce the error message, don't reproduce the error message -- you can't learn about the error message from those :)

      diagnostics/perldiag/splain 

       perl -we" my $foo = 1; my $foo = 2; "
"my" variable $foo masks earlier declaration in same scope at -e line 
+1.

$ perl -Mdiagnostics -we" my $foo = 1; my $foo = 2; "
"my" variable $foo masks earlier declaration in same scope at -e line 
+1 (#1)
    (W misc) A "my", "our" or "state" variable has been redeclared in 
+the
    current scope or statement, effectively eliminating all access to 
+the
    previous instance.  This is almost always a typographical error.  
+Note
    that the earlier variable will still exist until the end of the sc
+ope
    or until all closure referents to it are destroyed.

      [download]
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[d/l]
        ok i can understand that i have already declared $treeout before. But I think that all the information of the tree that i need is stored in $treeout and i cant use it. Just emptying $treeout with undef has no point at all.
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