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
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
