[Bioperl-l] problem parsing a newick format

[Mark A. Jensen]

Chrysanthi-
Do the trees in your test file end with a semicolon? When I do

use Bio::TreeIO;
$inp = Bio::TreeIO->new(-fh=>\*DATA, -format=>'newick);
$tre=$inp->next_tree;
__END__
(A:1,(B:2,C:3))

$tre is empty, but when

use Bio::TreeIO;
$inp = Bio::TreeIO->new(-fh=>\*DATA, -format=>'newick);
$tre=$inp->next_tree;
__END__
(A:1,(B:2,C:3));

$tre contains the tree.

If this is the problem, it sounds like a bug to me-
Mark
  ----- Original Message ----- 
  From: Chrysanthi A.
  To: Mark A. Jensen
  Cc: BioPerl List
  Sent: Thursday, February 12, 2009 5:42 AM
  Subject: Re: [Bioperl-l] problem parsing a newick format


  I tried also that, but it does not work.. It does not give me any error message.. It 
seems that the code is correct, but It does not print anything..Why???

  Thanks,

  Chrysanthi.




  2009/2/12 Mark A. Jensen <maj at fortinbras.us>

    C- I think you maybe want

    my $input = new Bio::TreeIO(-file =>"nexusCytochrome7R.newick",
                              -format => "newick");

    and not


      my $input = new Bio::TreeIO(-fh =>"nexusCytochrome7R.newick",
                                -format => "newick");


    ?

    Mark

    ----- Original Message ----- From: "Chrysanthi A." <chrysain at gmail.com>
    To: "BioPerl List" <bioperl-l at lists.open-bio.org>
    Sent: Wednesday, February 11, 2009 9:13 PM
    Subject: [Bioperl-l] problem parsing a newick format



      Is the code below correct?? Why it does not print anything???
      use strict;

      use Bio::TreeIO;


      my $input = new Bio::TreeIO(-fh =>"nexusCytochrome7R.newick",
                                -format => "newick");

      while(my $tree = $input->next_tree){
        for my $node(grep{!$_->is_Leaf}$tree->get_nodes){
      next if !$node->ancestor;
      print "Node:", $node->id, "length:", $node->branch_length, " ";
      for my $child($node->get_Descendents){
        print "child:", $child->id, "", $child->branch_length, " ";
      }
        print "\n";
        }
      }

      Any ideas? I want to read a tree and mainly get the duplication events.
      Could someone help me?

      Thanks a lot,

      Chrysanthi
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