[Bioperl-l] problem parsing a newick format

[Hilmar Lapp]

Note that the terminal semi-colon is part of the format spec. I've  
been bitten by this a few times in other programs - it's quite common  
that programs reading newick will throw an error or ignore the tree if  
it's not terminated by semi-colon.

Having said that, along the lines of being strict on what we emit but  
liberal in what we accept, I guess it can be loosened up. But what if  
there is more than one tree in the file?

	-hilmar

On Feb 12, 2009, at 8:03 AM, Mark A. Jensen wrote:

> 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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>
>
>
>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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