<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Tue, Aug 26, 2014 at 3:42 AM, <span dir="ltr"><<a href="mailto:def87@gmx.de" target="_blank">def87@gmx.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div>Hi,</div>
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<div>I am trying to do a tree traversal with the phylo package (just loop over every node). I have read the tree into a Newick tree object. Now the class docu of TreeMixin shows me the available methods: _filter_search seems to be what I need because it says that it's for tree traversals. However I don't want to apply a filter because I want to loop over every node in the tree. That will probably be easy to realize after having understood how _filter_search works (something like filter = 1 = true for all = loop over all nodes). But there is no documentation for this function and I don't understand how it works by just reading what its arguments are:</div>
<div><span><span>_filter_search(self</span>, <span>filter_func</span>, <span>order</span>, <span>follow_attrs</span>)</span></div>
<div>Could someone please tell me how to loop over every node (I need each node as a clade object, something like "for node in tree:")? I couldn't find anything regarding _filter_search in the cookbook.</div>
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<div>Regards,</div>
<div>Robert</div>
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</blockquote></div><br></div><div class="gmail_extra">Hi Robert,<br><br>The method to traverse a Newick tree is called find_clades():<br><a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec237">http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec237</a><br>
<br></div><div class="gmail_extra">Example:<br><br></div><div class="gmail_extra">from Bio import Phylo<br>tree = Phylo.read("example.nwk", "newick")<br></div><div class="gmail_extra">for clade in tree.find_clades(): print <a href="http://clade.name">clade.name</a><br>
</div><div class="gmail_extra"><br></div><div class="gmail_extra"><br></div><div class="gmail_extra">I see now that this isn't explained very well in the tutorial; sorry about that.<br></div><div class="gmail_extra">
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</div><div class="gmail_extra">All the best,<br>Eric<br></div></div>