A python module to read and write the Newick format
Project description
python-newick
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 u'F' >>> [n.name for n in trees[0].descendants] [u'A', u'B', u'E']
- From a
file
-like object:
>>> import io >>> from newick import load >>> with io.open('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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