<div dir="ltr">Dear Julien,<div><br></div><div>I <b>think</b> you can use</div><div><br></div><div><span style="font-size:13px">my $tax_level = $tree-></span>species_tree_node()->node_name();<br></div><div><br></div><div>or </div><div><br></div><div><span style="font-size:13px">my $tax_level = $tree-></span>taxonomy_level();<br></div><div><br></div><div>Cheers,</div><div><br>Steve</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 18 December 2014 at 13:42, Julien Roux <span dir="ltr"><<a href="mailto:julien.roux@unil.ch" target="_blank">julien.roux@unil.ch</a>></span> wrote:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear list,<br>
<br>
I used to get the taxonomical level of a gene tree using the following command:<br>
my $tax_level = $tree->get_tagvalue("taxon_<u></u>name");<br>
But now I get this message:<br>
----------------- DEPRECATED ---------------------<br>
Deprecated method call in file <a href="http://test.pl" target="_blank">test.pl</a> line 60.<br>
Method Bio::EnsEMBL::Compara::<u></u>GeneTreeNode::get_tagvalue is deprecated.<br>
The taxon_name tag has been deprecated, support will end with e78. Please use species_tree_node() from the gene-tree node to get taxon information<br>
<br>
I tried the following command without success:<br>
my $tax_level = $tree->species_tree_node->get_<u></u>tagvalue("taxon_id");<br>
my $tax_level = $tree->species_tree_node->get_<u></u>tagvalue("taxon_name");<br>
my $tax_level = ${$tree->species_tree_node}{"<u></u>taxon_id"};<br>
<br>
Any hint how to access this data?<br>
Thanks a lot<span class="HOEnZb"><font color="#888888"><br>
Julien<br>
<br>
-- <br>
Julien Roux<br>
Marie-Curie postdoctoral fellow<br>
Department of Ecology and Evolution, University of Lausanne, Switzerland<br>
<a href="http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html" target="_blank">http://www.unil.ch/dee/home/<u></u>menuinst/people/post-docs--<u></u>associates/dr-julien-roux.html</a><br>
Tel: <a href="tel:%2B41%2078%20700%202931" value="+41787002931" target="_blank">+41 78 700 2931</a><br>
<br>
<br>
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