Example #1
0
 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
Example #2
0
 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