[Bioperl-l] problem parsing a newick format

[Mark A. Jensen]

No problem, Chyrsanthi--

Jason-- may I loosen up the parser a bit on this?
MAJ
  ----- Original Message ----- 
  From: Chrysanthi A.
  To: Mark A. Jensen
  Sent: Thursday, February 12, 2009 7:47 AM
  Subject: Re: [Bioperl-l] problem parsing a newick format


  Yes, that was the problem.. Now its working perfect!!!! Thanks a lot!

  Chrysanthi


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

    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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