A nexus (phylogenetics) file reader (.nex, .trees)

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  • License: BSD License (BSD)
  • Author: Simon Greenhill
  • Tags phylogenetics, nexus, newick, paup, splitstree
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Reading a Nexus

>>> import os
>>> EXAMPLE_DIR = os.path.join(os.path.dirname(__file__), 'examples')
>>>
>>> from nexus import NexusReader
>>> n = NexusReader()
>>> n.read_file(os.path.join(EXAMPLE_DIR, 'example.nex'))
...
>>> n = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
...

# display blocks found in data file >>> n.blocks {‘data’: <NexusDataBlock: 2 characters from 4 taxa>}

data blocks

>>> n.data.nchar
2

>>> n.data.ntaxa
4

>>> n.data.format
{'datatype': 'standard', 'symbols': '01', 'gap': '-'}

>>> n.data.matrix.keys()
['Simon', 'Louise', 'Betty', 'Harry']

>>> n.data.matrix['Simon']
['0', '1']

>>> sorted(n.data.taxa)
['Betty', 'Harry', 'Louise', 'Simon']

>>> sorted(n.data.matrix.keys())
['Betty', 'Harry', 'Louise', 'Simon']

>>> for taxon, characters in n.data: #doctest: +SKIP

tree blocks

>>> n = NexusReader(os.path.join(EXAMPLE_DIR, 'example.trees'))
>>> n.trees.ntrees
3
>>> n.trees.trees[0][0:60]
'tree tree.0.1065.603220 = (((((((Chris:0.0668822155,Bruce:0.'

>>> for tree in n.trees: #doctest: +SKIP

Writing a Nexus File

>>> from nexus import NexusWriter
>>> n = NexusWriter()

Add a comment to appear in the header of the file >>> n.add_comment(“I am a comment”)

data are added by using the “add” function - which takes 3 arguments, a taxon, a character name, and a value

>>> n.add('taxon1', 'Character1', 'A')
>>> n.data
{'Character1': {'taxon1': 'A'}}
>>> n.add('taxon2', 'Character1', 'C')
>>> n.add('taxon3', 'Character1', 'A')

Characters and values can be strings or integers >>> n.add(‘taxon1’, 2, 1) >>> n.add(‘taxon2’, 2, 2) >>> n.add(‘taxon3’, 2, 3)

NexusWriter will interpolate missing entries (i.e. taxon2 in this case) >>> n.add(‘taxon1’, “Char3”, ‘4’) >>> n.add(‘taxon3’, “Char3”, ‘4’)

… when you’re ready, you can generate the nexus using make_nexus or write_to_file: n.make_nexus(interleave=True, charblock=True) n.write_to_file(filename=”output.nex”, interleave=True, charblock=True)

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