def testCalculateDupsAndLossesByReconcilingTrees_Examples(self):
treeString = '(((((((((((((human:0.006969,chimp:0.009727):0.025291,((baboon:0.008968):0.011019):0.024581):0.023649):0.066673):0.018405,((rat:0.081244,mouse:0.072818):0.238435):0.021892):0.02326,(((cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.004663):0.010883):0.033242):0.028346):0.016015):0.226853):0.063898):0.126639):0.119814):0.16696);'
speciesTree = newickTreeParser(treeString)
binaryTree_depthFirstNumbers(speciesTree)
#s = printBinaryTree(speciesTree, True)
#speciesTree = newickTreeParser(s)
#binaryTree_depthFirstNumbers(speciesTree)
geneString1 = ('((human,baboon),chimp);', 1, 3)
geneString2 = ('((human,chimp),baboon);', 0, 0)
geneString3 = ('((human,(human, chimp)),baboon);', 1, 1)
geneString4 = ('((human,(human, chimp)),(chimp, baboon));', 2, 3)
geneString5 = ('(dog,cat);', 0, 0)
geneString6 = ('((dog,cat), cow);', 0, 0)
geneString7 = ('(cow,(dog,cat));', 0, 0)
geneString8 = ('(cow,(cat,dog));', 0, 0)
geneString9 = ('((cow,dog),(dog,cow));', 1, 2)
geneString10 = ('((cow,(cow,cow)),(dog,cat));', 2, 0)
geneString11 = ('((cow,(cow,cow)),(dog,((cat,cat),cat)));', 4, 0)
geneStrings = [ geneString1, geneString2, geneString3, geneString4, \
geneString5, geneString6, geneString7, geneString8,
geneString9, geneString10, geneString11 ]
print ""
for geneString, dupCount, lossCount in geneStrings:
geneTree = newickTreeParser(geneString)
binaryTree_depthFirstNumbers(geneTree)
print printBinaryTree(geneTree, True), printBinaryTree(speciesTree, True)
dupCount2, lossCount2 = calculateDupsAndLossesByReconcilingTrees(speciesTree, geneTree, processID=lambda x : x)
print geneString, "dups", dupCount, dupCount2, "losses", lossCount, lossCount2
assert dupCount == dupCount2
assert lossCount == lossCount2
def testCalculateProbableRootOfGeneTree_Examples(self):
#return
treeString = '(((((((((((((human:0.006969,chimp:0.009727):0.025291,((baboon:0.008968):0.011019):0.024581):0.023649):0.066673):0.018405,((rat:0.081244,mouse:0.072818):0.238435):0.021892):0.02326,(((cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.004663):0.010883):0.033242):0.028346):0.016015):0.226853):0.063898):0.126639):0.119814):0.16696);'
speciesTree = newickTreeParser(treeString)
binaryTree_depthFirstNumbers(speciesTree)
geneString1 = ('((human,baboon),chimp);', '((human,chimp),baboon);')
geneString2 = ('((human,chimp),baboon);', '((human,chimp),baboon);')
geneString3 = ('((((human,chimp),baboon),((dog,cat),cow)),(mouse,rat));', '((((human,chimp),baboon),(mouse,rat)),((dog,cat),cow));')
geneString4 = ('((((human,chimp),baboon),(mouse,rat)),((dog,cat),cow));', '((((human,chimp),baboon),(mouse,rat)),((dog,cat),cow));')
geneString5 = ('((((human,(chimp, chimp)),baboon),((dog,cat),cow)),(mouse,rat));', '((((human,(chimp,chimp)),baboon),(mouse,rat)),((dog,cat),cow));')
#geneString3 = ('((human,(human, chimp)),baboon);', 1)
#geneString4 = ('((human,(human, chimp)),(chimp, baboon));', 2)
#geneString5 = ('(dog,cat);', 0)
#geneString6 = ('((dog,cat), cow);', 0)
#geneString7 = ('(cow,(dog,cat));', 0)
#geneString8 = ('(cow,(cat,dog));', 0)
#geneString9 = ('((cow,dog),(dog,cow));', 1)
#geneString10 = ('((cow,(cow,cow)),(dog,cat));', 2)
#geneString11 = ('((cow,(cow,cow)),(dog,((cat,cat),cat)));', 4)
geneStrings = [ geneString1, geneString2, geneString3, geneString4, geneString5 ]
#[ geneString3, geneString4, \
#geneString5, geneString6, geneString7, geneString8,
#geneString9, geneString10, geneString11 ]
for geneString, rootedGeneString in geneStrings:
geneTree = newickTreeParser(geneString)
rootedGeneTree = newickTreeParser(geneString)
binaryTree_depthFirstNumbers(geneTree)
rootedGeneTree2, dupCount, lossCount = calculateProbableRootOfGeneTree(speciesTree, geneTree)
print "rootedGeneTree", rootedGeneString, dupCount, lossCount, printBinaryTree(rootedGeneTree2, False)
def testMoveRoot(self):
for test in xrange(0, self.testNo):
binaryTree = getRandomTree()
binaryTree_depthFirstNumbers(binaryTree)
node = getRandomNode(binaryTree)
print "before", printBinaryTree(binaryTree, True), printBinaryTree(node, True)
remodTree = moveRoot(binaryTree, node.traversalID.mid)
print "test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True)
binaryTree_depthFirstNumbers(remodTree)
def testMoveRoot(self):
for test in xrange(0, self.testNo):
binaryTree = getRandomTree()
binaryTree_depthFirstNumbers(binaryTree)
node = getRandomNode(binaryTree)
print "before", printBinaryTree(binaryTree,
True), printBinaryTree(node, True)
remodTree = moveRoot(binaryTree, node.traversalID.mid)
print "test", test, printBinaryTree(
binaryTree,
True), printBinaryTree(node,
True), printBinaryTree(remodTree, True)
binaryTree_depthFirstNumbers(remodTree)
def testCalculateDupsAndLossesByReconcilingTrees(self):
for test in xrange(0, self.testNo):
speciesTree = getRandomTree()
binaryTree_depthFirstNumbers(speciesTree)
geneTree = getRandomTree()
binaryTree_depthFirstNumbers(geneTree)
l = [-1]
def fn():
l[0] += 1
return str(l[0])
labelTree(speciesTree, fn)
def fn2():
return str(int(l[0]*random.random()))
labelTree(geneTree, fn2)
calculateDupsAndLossesByReconcilingTrees(speciesTree, geneTree, processID=lambda x : x)
def testRemodelTreeRemovingRoot(self):
for test in xrange(0, self.testNo):
binaryTree = getRandomTree()
binaryTree_depthFirstNumbers(binaryTree)
node = getRandomLeafNode(binaryTree)
remodTree = remodelTreeRemovingRoot(binaryTree, node.traversalID.mid)
print "test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True)
binaryTree_depthFirstNumbers(remodTree)
distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)
d = getDistancesBetweenLeaves(binaryTree)
d2 = getDistancesBetweenLeaves(remodTree)
print d
print d2
for key in d2:
assert close(d2[key], d[key], 0.0001)
def testCalculateProbableRootOfGeneTree(self):
for test in xrange(0, self.testNo):
speciesTree = getRandomTree()
binaryTree_depthFirstNumbers(speciesTree)
geneTree = getRandomTree()
binaryTree_depthFirstNumbers(geneTree)
l = [-1]
def fn():
l[0] += 1
return str(l[0])
labelTree(speciesTree, fn)
def fn2():
return str(int(l[0]*random.random()))
labelTree(geneTree, fn2)
calculateProbableRootOfGeneTree(speciesTree, geneTree)
def testRemodelTreeRemovingRoot(self):
for test in xrange(0, self.testNo):
binaryTree = getRandomTree()
binaryTree_depthFirstNumbers(binaryTree)
node = getRandomLeafNode(binaryTree)
remodTree = remodelTreeRemovingRoot(binaryTree,
node.traversalID.mid)
print "test", test, printBinaryTree(
binaryTree,
True), printBinaryTree(node,
True), printBinaryTree(remodTree, True)
binaryTree_depthFirstNumbers(remodTree)
distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)
d = getDistancesBetweenLeaves(binaryTree)
d2 = getDistancesBetweenLeaves(remodTree)
print d
print d2
for key in d2:
assert close(d2[key], d[key], 0.0001)
def testCalculateProbableRootOfGeneTree(self):
for test in xrange(0, self.testNo):
speciesTree = getRandomTree()
binaryTree_depthFirstNumbers(speciesTree)
geneTree = getRandomTree()
binaryTree_depthFirstNumbers(geneTree)
l = [-1]
def fn():
l[0] += 1
return str(l[0])
labelTree(speciesTree, fn)
def fn2():
return str(int(l[0] * random.random()))
labelTree(geneTree, fn2)
calculateProbableRootOfGeneTree(speciesTree, geneTree)
def testCalculateProbableRootOfGeneTree_Examples(self):
#return
treeString = '(((((((((((((human:0.006969,chimp:0.009727):0.025291,((baboon:0.008968):0.011019):0.024581):0.023649):0.066673):0.018405,((rat:0.081244,mouse:0.072818):0.238435):0.021892):0.02326,(((cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.004663):0.010883):0.033242):0.028346):0.016015):0.226853):0.063898):0.126639):0.119814):0.16696);'
speciesTree = newickTreeParser(treeString)
binaryTree_depthFirstNumbers(speciesTree)
geneString1 = ('((human,baboon),chimp);', '((human,chimp),baboon);')
geneString2 = ('((human,chimp),baboon);', '((human,chimp),baboon);')
geneString3 = (
'((((human,chimp),baboon),((dog,cat),cow)),(mouse,rat));',
'((((human,chimp),baboon),(mouse,rat)),((dog,cat),cow));')
geneString4 = (
'((((human,chimp),baboon),(mouse,rat)),((dog,cat),cow));',
'((((human,chimp),baboon),(mouse,rat)),((dog,cat),cow));')
geneString5 = (
'((((human,(chimp, chimp)),baboon),((dog,cat),cow)),(mouse,rat));',
'((((human,(chimp,chimp)),baboon),(mouse,rat)),((dog,cat),cow));')
#geneString3 = ('((human,(human, chimp)),baboon);', 1)
#geneString4 = ('((human,(human, chimp)),(chimp, baboon));', 2)
#geneString5 = ('(dog,cat);', 0)
#geneString6 = ('((dog,cat), cow);', 0)
#geneString7 = ('(cow,(dog,cat));', 0)
#geneString8 = ('(cow,(cat,dog));', 0)
#geneString9 = ('((cow,dog),(dog,cow));', 1)
#geneString10 = ('((cow,(cow,cow)),(dog,cat));', 2)
#geneString11 = ('((cow,(cow,cow)),(dog,((cat,cat),cat)));', 4)
geneStrings = [
geneString1, geneString2, geneString3, geneString4, geneString5
]
#[ geneString3, geneString4, \
#geneString5, geneString6, geneString7, geneString8,
#geneString9, geneString10, geneString11 ]
for geneString, rootedGeneString in geneStrings:
geneTree = newickTreeParser(geneString)
rootedGeneTree = newickTreeParser(geneString)
binaryTree_depthFirstNumbers(geneTree)
rootedGeneTree2, dupCount, lossCount = calculateProbableRootOfGeneTree(
speciesTree, geneTree)
print "rootedGeneTree", rootedGeneString, dupCount, lossCount, printBinaryTree(
rootedGeneTree2, False)
def testCalculateDupsAndLossesByReconcilingTrees(self):
for test in xrange(0, self.testNo):
speciesTree = getRandomTree()
binaryTree_depthFirstNumbers(speciesTree)
geneTree = getRandomTree()
binaryTree_depthFirstNumbers(geneTree)
l = [-1]
def fn():
l[0] += 1
return str(l[0])
labelTree(speciesTree, fn)
def fn2():
return str(int(l[0] * random.random()))
labelTree(geneTree, fn2)
calculateDupsAndLossesByReconcilingTrees(speciesTree,
geneTree,
processID=lambda x: x)
def testCalculateDupsAndLossesByReconcilingTrees_Examples(self):
treeString = '(((((((((((((human:0.006969,chimp:0.009727):0.025291,((baboon:0.008968):0.011019):0.024581):0.023649):0.066673):0.018405,((rat:0.081244,mouse:0.072818):0.238435):0.021892):0.02326,(((cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.004663):0.010883):0.033242):0.028346):0.016015):0.226853):0.063898):0.126639):0.119814):0.16696);'
speciesTree = newickTreeParser(treeString)
binaryTree_depthFirstNumbers(speciesTree)
#s = printBinaryTree(speciesTree, True)
#speciesTree = newickTreeParser(s)
#binaryTree_depthFirstNumbers(speciesTree)
geneString1 = ('((human,baboon),chimp);', 1, 3)
geneString2 = ('((human,chimp),baboon);', 0, 0)
geneString3 = ('((human,(human, chimp)),baboon);', 1, 1)
geneString4 = ('((human,(human, chimp)),(chimp, baboon));', 2, 3)
geneString5 = ('(dog,cat);', 0, 0)
geneString6 = ('((dog,cat), cow);', 0, 0)
geneString7 = ('(cow,(dog,cat));', 0, 0)
geneString8 = ('(cow,(cat,dog));', 0, 0)
geneString9 = ('((cow,dog),(dog,cow));', 1, 2)
geneString10 = ('((cow,(cow,cow)),(dog,cat));', 2, 0)
geneString11 = ('((cow,(cow,cow)),(dog,((cat,cat),cat)));', 4, 0)
geneStrings = [ geneString1, geneString2, geneString3, geneString4, \
geneString5, geneString6, geneString7, geneString8,
geneString9, geneString10, geneString11 ]
print ""
for geneString, dupCount, lossCount in geneStrings:
geneTree = newickTreeParser(geneString)
binaryTree_depthFirstNumbers(geneTree)
print printBinaryTree(geneTree,
True), printBinaryTree(speciesTree, True)
dupCount2, lossCount2 = calculateDupsAndLossesByReconcilingTrees(
speciesTree, geneTree, processID=lambda x: x)
print geneString, "dups", dupCount, dupCount2, "losses", lossCount, lossCount2
assert dupCount == dupCount2
assert lossCount == lossCount2