[Bioperl-l] TreeIO for NHX format

Chris Fields cjfields at illinois.edu
Tue Oct 26 23:41:40 EDT 2010


Ameet,

You should file this as a bug, along with example code and data (http://bugzilla.open-bio.org/).  It's possible the tags are parsed but the NHX writer is not finding the data somehow.

chris

On Oct 26, 2010, at 6:51 PM, Ameet Talwalkar wrote:

> Hi,
> 
> I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
> format, and I have tried the following code:
> 
> *use Bio::TreeIO;
> 
> my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
>                            -format => "phyloxml");
> my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
>                              -format => 'nhx');
> 
> while (my $tree = $input->next_tree) {
>  $treeout->write_tree($tree);
> }
> *
> 
> The output is indeed in NHX format, but the tags (in particular I have a
> duplication / speciation tag) does not appear in the output.  Am I doing
> something wrong?
> 
> Thanks.
> 
> -Ameet
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