def test_root_midpt2(self):
""" midpoint between nodes should behave correctly"""
from qiime.make_phylogeny import root_midpt
from cogent.core.tree import PhyloNode
from qiime.parse import parse_newick
tree = parse_newick('(a:1,((c:1,d:2.5)n3:1,b:1)n2:1)rt;')
tmid = root_midpt(tree)
self.assertEqual(tmid.getDistances(), tree.getDistances())
tipnames = tree.getTipNames()
nontipnames = [t.Name for t in tree.nontips()]
self.assertTrue(tmid.isRoot())
self.assertEqual(tmid.distance(tmid.getNodeMatchingName('d')), 2.75)
def test_root_midpt2(self):
""" midpoint between nodes should behave correctly"""
from qiime.make_phylogeny import root_midpt
from cogent.core.tree import PhyloNode
from qiime.parse import parse_newick
tree = parse_newick('(a:1,((c:1,d:2.5)n3:1,b:1)n2:1)rt;')
tmid = root_midpt(tree)
self.assertEqual(tmid.getDistances(),tree.getDistances())
tipnames = tree.getTipNames()
nontipnames = [t.Name for t in tree.nontips()]
self.assertTrue(tmid.isRoot())
self.assertEqual(tmid.distance(tmid.getNodeMatchingName('d')), 2.75)
def test_root_midpt(self):
"""midpoint should be selected correctly when it is an internal node
"""
from qiime.make_phylogeny import root_midpt
from cogent.core.tree import PhyloNode
from qiime.parse import parse_newick
tree = parse_newick('(a:1,((c:1,d:3)n3:1,b:1)n2:1)rt;')
tmid = root_midpt(tree)
self.assertEqual(tmid.getDistances(), tree.getDistances())
tipnames = tree.getTipNames()
nontipnames = [t.Name for t in tree.nontips()]
# for tipname in tipnames:
# tmid_tip = tmid.getNodeMatchingName(tipname)
# orig_tip = tree.getNodeMatchingName(tipname)
# for nontipname in nontipnames:
# tmid_dist=\
# tmid.getNodeMatchingName(nontipname).distance(tmid_tip)
# orig_dist=\
# tree.getNodeMatchingName(nontipname).distance(orig_tip)
# print nontipname, tipname, 'assert'
# self.assertEqual(tmid_dist, orig_dist)
self.assertTrue(tmid.isRoot())
self.assertEqual(tmid.distance(tmid.getNodeMatchingName('d')), 3)
def test_root_midpt(self):
"""midpoint should be selected correctly when it is an internal node
"""
from qiime.make_phylogeny import root_midpt
from cogent.core.tree import PhyloNode
from qiime.parse import parse_newick
tree = parse_newick('(a:1,((c:1,d:3)n3:1,b:1)n2:1)rt;')
tmid = root_midpt(tree)
self.assertEqual(tmid.getDistances(),tree.getDistances())
tipnames = tree.getTipNames()
nontipnames = [t.Name for t in tree.nontips()]
# for tipname in tipnames:
# tmid_tip = tmid.getNodeMatchingName(tipname)
# orig_tip = tree.getNodeMatchingName(tipname)
# for nontipname in nontipnames:
# tmid_dist=\
# tmid.getNodeMatchingName(nontipname).distance(tmid_tip)
# orig_dist=\
# tree.getNodeMatchingName(nontipname).distance(orig_tip)
# print nontipname, tipname, 'assert'
# self.assertEqual(tmid_dist, orig_dist)
self.assertTrue(tmid.isRoot())
self.assertEqual(tmid.distance(\
tmid.getNodeMatchingName('d')), 3)
