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A python module to read and write the Newick format

Project description


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python package to read and write the Newick format.

Reading Newick

  • From a string:
>>> from newick import loads
>>> trees = loads('(A,B,(C,D)E)F;')
>>> trees[0].name
>>> [ for n in trees[0].descendants]
['A', 'B', 'E']
  • From a file-like object:
>>> import io
>>> from newick import load
>>> with'fname', encoding='utf8') as fp:
...     trees = load(fp)
  • From a file name:
>>> from newick import read
>>> trees = read('fname')

Writing Newick

In parallel to the read operations there are three functions to serialize a single Node object or a list of Node objects to Newick format:

  • dumps(trees) -> str
  • dump(trees, fp)
  • write(trees, 'fname')

A tree may be assembled using the factory methods of the Node class:

  • Node.__init__
  • Node.create
  • Node.add_descendant

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