def runAsMedianMedianProblemTest(medianHistory):
"""Runs AsMedian, requires to be installed. I got it from:
https://sites.google.com/site/andrewweixu/Home/software/asmedian
"""
#Dump to disk
tempFile = os.path.join(os.getcwd(), "simulatedGenomeTempFile.txt")
fileHandle = open(tempFile, 'w')
fileHandle.write(medianHistory.getLeafGenomeString())
fileHandle.close()
#-cp /Users/benedictpaten/Desktop/ASMedian-1.0
popenCatch("java BIOMedian %s" % tempFile)
os.remove(tempFile)
#Parse in
fileHandle = open(tempFile + ".rst", 'r')
input = fileHandle.readlines()
fileHandle.close()
os.remove(tempFile + ".rst")
asMedianMedianGenome = Genome(chromosomeNumber=0, elementNumber=0)
for line in input[1:]:
if line[0] == '#':
break
asMedianChromosome = Chromosome()
for element in line.split()[1:]:
asMedianChromosome.append(int(element))
asMedianMedianGenome.addChromosome(asMedianChromosome)
return asMedianMedianGenome
def runReferenceMedianProblemTest(medianHistory, greedyIterations, theta):
"""Runs the reference problem for a given median history
"""
#Make adjacencies
stubNumber = 2
nodeNumber = len(
medianHistory.getMedianGenome().getElements()) * 2 + stubNumber
weights = {}
for genome in medianHistory.getLeafGenomes():
for node1, node2, distance in genome.getTransitiveAdjacencies():
if (node1, node2) in weights:
weights[(node1, node2)] += weightFn(distance, theta)
else:
weights[(node1, node2)] = weightFn(distance, theta)
def translateLeftSideOfElementToNode(element):
assert element != 0
if element < 0:
return abs(element) * 2
return element * 2 + 1
def translateLeftNodeToElement(node):
assert node >= stubNumber
assert node < nodeNumber
element = node / 2
if (node % 2) == 0:
element *= -1
return element
#Now print out the
input = "%i\t%i\t%i\t%i\t%s" % (
greedyIterations, nodeNumber, stubNumber, len(weights.keys()),
"\t".join([
"%i\t%i\t%f" %
(translateLeftSideOfElementToNode(-node1),
translateLeftSideOfElementToNode(node2), weights[(node1, node2)])
for (node1, node2) in weights.keys()
]))
tempPath = getTempFile()
with open(tempPath, 'w') as tempFile:
tempFile.write(input)
#Command
command = os.path.join(
os.path.split(
os.path.abspath(
matchingAndOrdering.tests.simulatedGenome.__file__))[0],
"testBin", "referenceMedianProblemTest2")
output = popenCatch(command + " < %s" % tempPath)
os.remove(tempPath)
medianChromosome = Chromosome()
for adjacency in output.split():
medianChromosome.append(translateLeftNodeToElement(int(adjacency)))
medianGenome = Genome(chromosomeNumber=0, elementNumber=0)
medianGenome.addChromosome(medianChromosome)
assert medianGenome.getElements() == medianHistory.getMedianGenome(
).getElements()
return medianGenome
def testGenome(self):
"""Test basic functions of a genome
"""
d = Genome(elementNumber=10, chromosomeNumber=3)
self.assertEqual(d.getChromosomeNumber(), 3)
self.assertEqual(d.getElements(), set(range(1, 11)))
#Test clone
self.assertEqual(str(d), str(d.clone()))
#Test inversions
for i in xrange(100):
e = d.clone()
self.assertEquals(d.getOutOfOrderDistance(e), 0)
self.assertEquals(d.getCircularDcjDistance(e), 0)
e.permuteByInversion()
self.assertEquals(e.getChromosomeNumber(), 3)
self.assertEquals(e.getElements(), d.getElements())
self.assertTrue(d.getOutOfOrderDistance(e) >= 0)
self.assertTrue(d.getCircularDcjDistance(e) in [0, 1])
#Test dcj
for i in xrange(100):
e = d.clone()
self.assertEquals(d.getOutOfOrderDistance(e), 0)
self.assertEquals(d.getCircularDcjDistance(e), 0)
e.permuteByDcj()
self.assertEquals(e.getElements(), d.getElements())
self.assertTrue(d.getOutOfOrderDistance(e) >= 0)
self.assertTrue(d.getCircularDcjDistance(e) in [0, 1, 2])
#Test translocations
for i in xrange(100):
e = d.clone()
self.assertEquals(d.getOutOfOrderDistance(e), 0)
self.assertEquals(d.getCircularDcjDistance(e), 0)
e.permuteByTranslocation()
self.assertEquals(e.getElements(), d.getElements())
self.assertTrue(d.getOutOfOrderDistance(e) >= 0)
self.assertTrue(d.getCircularDcjDistance(e) in [0, 1, 2])
def testReferenceAndAsMedianAlgorithms(self):
"""Iterates through a list of simulation variants and prints results
"""
headerLine = "\t".join(
("elementNumber", "chromosomeNumber", "leafGenomeNumber",
"operationNumber", "totalOperationNumber", "doInversion",
"doShortInversion", "doDcj", "doTranslocation",
"doShortTranslocation", "greedyIterations", "theta", "replicate",
"medianDCJDistance", "medianOutOfOrderDistance",
"weightedMedianOutOfOrderDistance",
"medianDCJDistanceForReferenceAlgorithm",
"medianOutOfOrderDistanceForReferenceAlgorithm",
"weightedMedianOutOfOrderDistanceForReferenceAlgorithm",
"dCJDistanceForReferenceAlgorithmFromMedian",
"outOfOrderDistanceForReferenceAlgorithmFromMedian",
"weightedOutOfOrderDistanceForReferenceAlgorithmFromMedian",
"medianDCJDistanceForAsMedian",
"medianOutOfOrderDistanceForAsMedian",
"weightedMedianOutOfOrderDistanceForAsMedian",
"dCJDistanceForAsMedianFromMedian",
"outOfOrderDistanceForAsMedianFromMedian",
"weightedOutOfOrderDistanceForAsMedianFromMedian",
"medianGenomeForReferenceAlgorithm", "medianGenomeForAsMedian"))
if getLogLevelString() in ("DEBUG", "INFO"):
print headerLine
for elementNumber in self.elementNumbers:
for chromosomeNumber in self.chromosomeNumbers:
for leafGenomeNumber in self.leafGenomeNumbers:
for operationNumber in self.operationNumber:
for doInversion, doShortInversion, doDcj, doTranslocation, doShortTranslocation in self.operationType:
for greedyIterations in self.greedyIterations:
for theta in self.theta:
for replicate in xrange(self.replicates):
medianHistory = MedianHistory(
Genome(elementNumber=elementNumber,
chromosomeNumber=
chromosomeNumber),
leafGenomeNumber=leafGenomeNumber)
medianHistory.permuteLeafGenomes(
operationNumber=operationNumber,
doInversion=doInversion,
doDcj=doDcj,
doTranslocation=doTranslocation,
doShortInversion=doShortInversion,
doShortTranslocation=
doShortTranslocation)
medianDCJDistance = medianHistory.getMedianDcjDistance(
medianHistory.getMedianGenome())
medianOutOfOrderDistance = medianHistory.getMedianOutOfOrderDistance(
medianHistory.getMedianGenome())
weightedMedianOutOfOrderDistance = medianHistory.getWeightedMedianOutOfOrderDistance(
medianHistory.getMedianGenome(),
theta=theta)
#Now run reference problem algorithm
referenceProblemMedianGenome = runReferenceMedianProblemTest(
medianHistory, greedyIterations,
theta)
medianDCJDistanceForReferenceAlgorithm = medianHistory.getMedianDcjDistance(
referenceProblemMedianGenome)
medianOutOfOrderDistanceForReferenceAlgorithm = medianHistory.getMedianOutOfOrderDistance(
referenceProblemMedianGenome)
weightedMedianOutOfOrderDistanceForReferenceAlgorithm = medianHistory.getWeightedMedianOutOfOrderDistance(
referenceProblemMedianGenome,
theta=theta)
dCJDistanceForReferenceAlgorithmFromMedian = medianHistory.getMedianGenome(
).getCircularDcjDistance(
referenceProblemMedianGenome)
outOfOrderDistanceForReferenceAlgorithmFromMedian = medianHistory.getMedianGenome(
).getOutOfOrderDistance(
referenceProblemMedianGenome)
weightedOutOfOrderDistanceForReferenceAlgorithmFromMedian = medianHistory.getMedianGenome(
).getWeightedOutOfOrderDistance(
referenceProblemMedianGenome,
theta=theta)
totalOperationNumber = operationNumber * len(
[
i for i in
(doInversion, doShortInversion,
doDcj, doTranslocation,
doShortTranslocation)
if i == True
])
#Biomedian comparison turned off
if False and leafGenomeNumber == 3 and doDcj == False and float(
totalOperationNumber
) / elementNumber <= 0.5:
asMedianProblemMedianGenome = runAsMedianMedianProblemTest(
medianHistory)
medianDCJDistanceForAsMedian = medianHistory.getMedianDcjDistance(
asMedianProblemMedianGenome)
medianOutOfOrderDistanceForAsMedian = medianHistory.getMedianOutOfOrderDistance(
asMedianProblemMedianGenome)
weightedMedianOutOfOrderDistanceForAsMedian = medianHistory.getWeightedMedianOutOfOrderDistance(
asMedianProblemMedianGenome,
theta=theta)
dCJDistanceForAsMedianFromMedian = medianHistory.getMedianGenome(
).getCircularDcjDistance(
asMedianProblemMedianGenome)
outOfOrderDistanceForAsMedianFromMedian = medianHistory.getMedianGenome(
).getOutOfOrderDistance(
asMedianProblemMedianGenome)
weightedOutOfOrderDistanceForAsMedianFromMedian = medianHistory.getMedianGenome(
).getWeightedOutOfOrderDistance(
asMedianProblemMedianGenome,
theta=theta)
else:
asMedianProblemMedianGenome = "n/a"
medianDCJDistanceForAsMedian = "n/a"
medianOutOfOrderDistanceForAsMedian = "n/a"
weightedMedianOutOfOrderDistanceForAsMedian = "n/a"
dCJDistanceForAsMedianFromMedian = "n/a"
outOfOrderDistanceForAsMedianFromMedian = "n/a"
weightedOutOfOrderDistanceForAsMedianFromMedian = "n/a"
#Now prepare line to print
line = "\t".join([
str(i) for i in
(elementNumber, chromosomeNumber,
leafGenomeNumber, operationNumber,
totalOperationNumber, doInversion,
doShortInversion, doDcj,
doTranslocation,
doShortTranslocation,
greedyIterations, theta,
replicate, medianDCJDistance,
medianOutOfOrderDistance,
weightedMedianOutOfOrderDistance,
medianDCJDistanceForReferenceAlgorithm,
medianOutOfOrderDistanceForReferenceAlgorithm,
weightedMedianOutOfOrderDistanceForReferenceAlgorithm,
dCJDistanceForReferenceAlgorithmFromMedian,
outOfOrderDistanceForReferenceAlgorithmFromMedian,
weightedOutOfOrderDistanceForReferenceAlgorithmFromMedian,
medianDCJDistanceForAsMedian,
medianOutOfOrderDistanceForAsMedian,
weightedMedianOutOfOrderDistanceForAsMedian,
dCJDistanceForAsMedianFromMedian,
outOfOrderDistanceForAsMedianFromMedian,
weightedOutOfOrderDistanceForAsMedianFromMedian,
"'%s'" %
str(referenceProblemMedianGenome),
"'%s'" %
str(asMedianProblemMedianGenome))
])
#Print line
if getLogLevelString() in ("DEBUG",
"INFO"):
print line
