def init(self, **kwargs):
"""Valid keyword arguments include filename, format, newick, taxon_labels, trees and title.
filename should be a string and should represent the path to a tree file.
format is relevant only if filename is specified. The values for format are
in the FileFormats class (but currently include only FileFormats.NEXUS).
newick is a newick string representation of a tree topology (with or without
edge lengths).
taxon_labels provide names for the numbers used in a newick description (alternatively,
taxon labels can be provided directly in the newick string)
trees is an iterable collection of phylogeny.Tree objects.
title is a label for the collection.
"""
self.reset()
self.title = kwargs.get("title")
self.filename = kwargs.get("filename")
if self.filename is None:
self.filename = kwargs.get("file")
if self.filename:
self.format = kwargs.get("format", FileFormats.NEXUS)
self.trees = []
self.taxon_labels = None
else:
self.format = None
self.taxon_labels = kwargs.get("taxon_labels")
newick = kwargs.get("newick")
if newick:
if not isinstance(newick, Newick):
newick = Newick(newick)
tree = phylogeny.Tree()
# by default the tree is read as 1-based (as in NEXUS trees)
newick.buildTree(tree)
self.trees = [tree]
else:
self.trees = kwargs.get("trees", [])
self.active_taxa = self.taxon_labels
def _simulateTree(self):
if (not self.taxon_labels) and self.n_taxa < 1 and (not self.newick):
raise ValueError("TreeSimulator cannot be created with an empty list of taxon_labels and n_taxa set to 0")
tl = self.taxon_labels
if tl:
t = Phylogeny.Tree(taxon_labels=self.taxon_labels)
ntax = len(self.taxon_labels)
else:
t = Phylogeny.Tree()
ntax = self.n_taxa
tm = Phylogeny.TreeManip(t)
eld = self.edgelen_dist
self.stdout.debugging("RandomTree._simulateTree seed = %d" % self.r.getSeed())
n = self.newick
if n:
if not isinstance(n, Newick):
n = Newick(n)
n.buildTree(t)
tm.setRandomEdgeLengths(self.edgelen_dist)
elif self.distribution.lower() == "yule":
if eld is None:
isp = self.speciation_rate
if isp is None or isp <= 0.0:
raise ValueError(
"edgelen_dist or the speciation_rate must be set to generate trees from the Yule process"
)
eld = Exponential(isp)
eld.setLot(self.r)
self.stdout.debugging("Calling TreeManip.yuleTree")
tm.yuleTree(ntax, self.r, eld)
else:
self.stdout.debugging("Calling TreeManip.randTree")
tm.randTree(ntax, self.r, eld)
else:
self.stdout.debugging("Calling TreeManip.equiprobTree")
tm.equiprobTree(ntax, self.r, eld)
return t