예제 #1
0
 def getAlignable(self, aligned_positions, ratio=None):
     assert ratio is None, "already 2-branched"
     children = self.pair.children # alignables
     leaves = [c.leaf for c in children]
     aligned_positions = [posn for (bin, posn) in aligned_positions]
     pog = self.pair.getPOG(aligned_positions)
     edge = LikelihoodTreeEdge(leaves, 'parent', pog.getAlignedPositions())
     (plhs, gapscores) = self.makePartialLikelihoods(use_cost_function=False)
     plh = self.pair.edge2plh(edge, plhs)
     assert len(plh) == 1, ('bins!', len(plh))
     leaf = edge.asLeaf(plh[0]) # like profile
     return AlignablePOG(leaf, pog, children)
예제 #2
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파일: pairwise.py 프로젝트: miklou/pycogent
 def getAlignable(self, aligned_positions, ratio=None):
     assert ratio is None, "already 2-branched"
     children = self.pair.children # alignables
     leaves = [c.leaf for c in children]
     aligned_positions = [posn for (bin, posn) in aligned_positions]
     pog = self.pair.getPOG(aligned_positions)
     edge = LikelihoodTreeEdge(leaves, 'parent', pog.getAlignedPositions())
     (plhs, gapscores) = self.makePartialLikelihoods(use_cost_function=False)
     plh = self.pair.edge2plh(edge, plhs)
     assert len(plh) == 1, ('bins!', len(plh))
     leaf = edge.asLeaf(plh[0]) # like profile
     return AlignablePOG(leaf, pog, children)
예제 #3
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def recursive_lht_build(edge, leaves):
    if edge.istip():
        lhe = leaves[edge.Name]
    else:
        lht_children = []
        for child in edge.Children:
            lht = recursive_lht_build(child, leaves)
            lht_children.append(lht)
        lhe = LikelihoodTreeEdge(lht_children, edge_name=edge.Name)
    return lhe