[Biopython-dev] [Biopython - Bug #3408] (New) Parsing of Nexus files generated by TreeBase fails (Bio.Phylo)

[redmine at redmine.open-bio.org]

Issue #3408 has been reported by Ben Morris.

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Bug #3408: Parsing of Nexus files generated by TreeBase fails (Bio.Phylo)
https://redmine.open-bio.org/issues/3408

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


Steps to reproduce: 

Pick a tree on TreeBase (e.g. http://treebase.org/treebase-web/search/study/trees.html?id=12003 or http://treebase.org/treebase-web/search/study/trees.html?id=1029) and click on "download reconstructed NEXUS file."

Attempt to parse the file using Bio.Phylo.read.

Exception:

<pre>Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 62, in read
    tree = tree_gen.next()
  File "/usr/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 50, in parse
    for tree in getattr(supported_formats[format], 'parse')(fp, **kwargs):
  File "/usr/lib/python2.7/site-packages/Bio/Phylo/NexusIO.py", line 39, in parse
    nex = Nexus.Nexus(handle)
  File "/usr/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 572, in __init__
    self.read(input)
  File "/usr/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 623, in read
    self._parse_nexus_block(title, contents)
  File "/usr/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 664, in _parse_nexus_block
    getattr(self,'_'+line.command)(line.options)
AttributeError: 'Nexus' object has no attribute '_link'
</pre>


DendroPy is able to parse the same files.


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