[Bioperl-l] problem parsing a newick format

[Chrysanthi A.]

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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>>
>>
>>