Duplicate labels about dendropy

[jeetsukumaran]

Hi,

Unfortunately, despite the promise of this keyword in the function
signature, this feature is not properly implemented in DendroPy 3. It
will be in DendroPy 4. Once I release DendroPy 4, I may back-port
support for this in DendroPy 3. In the mean time, is it possible for you
to pre-process the file to ensure distinct labels?

On 4/11/14, 8:43 AM, namphuon wrote:

Trying to read a tree with duplicate labels fails.

If I have test.out containing
((a,a),(b,c));

The following line:
trees =
dendropy.TreeList.get_from_path('test.out','newick',allow_duplicate_taxon_labels=True)

outputs:
Traceback (most recent call last):
File "", line 1, in
File
"python/lib/python2.7/site-packages/DendroPy-3.12.0-py2.7.egg/dendropy/dataobject/tree.py",
line 641, in init
self.process_source_kwargs(**kwargs)
File
"python/lib/python2.7/site-packages/DendroPy-3.12.0-py2.7.egg/dendropy/utility/iosys.py",
line 285, in process_source_kwargs
self.read(stream=stream, schema=schema, *_kwargs)
File
"python/lib/python2.7/site-packages/DendroPy-3.12.0-py2.7.egg/dendropy/dataobject/tree.py",
line 701, in read
tree = Tree./parse_from_stream(stream, schema, *_kwargs)
File
"python/lib/python2.7/site-packages/DendroPy-3.12.0-py2.7.egg/dendropy/dataobject/tree.py",
line 485, in /parse_from_stream
d = DataSet(stream=stream, schema=schema, **kwargs)
File
"python/lib/python2.7/site-packages/DendroPy-3.12.0-py2.7.egg/dendropy/dataobject/dataset.py",
line 88, in __init//
self.process_source_kwargs(**kwargs)
File
"python/lib/python2.7/site-packages/DendroPy-3.12.0-py2.7.egg/dendropy/utility/iosys.py",
line 285, in process_source_kwargs
self.read(stream=stream, schema=schema, **kwargs)
File
"python/lib/python2.7/site-packages/DendroPy-3.12.0-py2.7.egg/dendropy/dataobject/dataset.py",
line 165, in read
raise x
dendropy.utility.error.DataParseError: Error parsing data source
"test.out" on line 1 at column 7: Taxon a used twice (it appears as a
the second time)

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Jeet Sukumaran

[email protected]

Department of Biology
Duke University
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Durham, NC 27708

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[jeetsukumaran]

This is implemented in DendroPy 4 by using suppress_internal_node_taxa=True and suppress_external_node_taxa=True keyword arguments to for the labels to be interpreted as node labels rather than taxon labels.