[Biopython-dev] [Biopython - Bug #3316] (New) Phylo/NewickIO fails to write non-leaf names with newick output

[redmine at redmine.open-bio.org]

Issue #3316 has been reported by Nicola Segata.

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Bug #3316: Phylo/NewickIO fails to write non-leaf names with newick output
https://redmine.open-bio.org/issues/3316

Author: Nicola Segata
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


If I read the following newick tree
<pre>
(A,B,(C,D)E)F;
</pre>
and then I write it again in newick format I get
<pre>
(A:1.00000,B:1.00000,(C:1.00000,D:1.00000):1.00000):1.00000;
</pre>
which is missing the names of the internal nodes E and F.
If I export it in PhyloXML I get the right names:
<pre>
<phy:phyloxml xmlns:phy="http://www.phyloxml.org">
  <phy:phylogeny rooted="false">
    <phy:name />
    <phy:clade>
      <phy:name>pippol</phy:name>
      <phy:branch_length>1.0</phy:branch_length>
      <phy:clade>
        <phy:name>A</phy:name>
        <phy:branch_length>1.0</phy:branch_length>
      </phy:clade>
      <phy:clade>
        <phy:name>B</phy:name>
        <phy:branch_length>1.0</phy:branch_length>
      </phy:clade>
      <phy:clade>
        <phy:name>E</phy:name>
        <phy:branch_length>1.0</phy:branch_length>
        <phy:clade>
          <phy:name>C</phy:name>
          <phy:branch_length>1.0</phy:branch_length>
        </phy:clade>
        <phy:clade>
          <phy:name>D</phy:name>
          <phy:branch_length>1.0</phy:branch_length>
        </phy:clade>
      </phy:clade>
    </phy:clade>
  </phy:phylogeny>

</pre>


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