[Biopython-dev] [Biopython - Bug #3409] (New) Newick parser fails to parse Greengenes tree (Bio.Phylo)

[redmine at redmine.open-bio.org]

Issue #3409 has been reported by Ben Morris.

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Bug #3409: Newick parser fails to parse Greengenes tree (Bio.Phylo)
https://redmine.open-bio.org/issues/3409

Author: Ben Morris
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


The file is available here: http://www.evoio.org/wg/evoio/images/f/f9/Greengenes2011.txt (9.2 MB)

The problem may be related to the use of single-quoted node labels which sometimes contain parentheses, e.g. <pre>'p__Fusobacteria; c__Fusobacteria (class); o__Fusobacteriales; f__Fusobacteriaceae':0.11021</pre>

Exception:

<pre>  ...
  File "/usr/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 110, in _parse_subtree
    clade.clades = [self._parse_subtree(st) for st in subtrees]
  File "/usr/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 110, in _parse_subtree
    clade.clades = [self._parse_subtree(st) for st in subtrees]
  File "/usr/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 110, in _parse_subtree
    clade.clades = [self._parse_subtree(st) for st in subtrees]
  File "/usr/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 110, in _parse_subtree
    clade.clades = [self._parse_subtree(st) for st in subtrees]
  File "/usr/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 87, in _parse_subtree
    raise NewickError("Parentheses do not match in (sub)tree: " + text)
Bio.Phylo.NewickIO.NewickError: Parentheses do not match in (sub)tree: 139839:0.04507):0.02429
</pre>

Other Newick parsers (ete and dendropy) are able to parse this file.


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