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 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 testChromosome(self):
"""Test basic functions of a chromosome.
"""
c = Chromosome()
#Append method
c.append(1)
c.append(2)
#Test string generator
self.assertEquals(c.getOrderedElements(), [1, 2])
self.assertEqual(str(c), "1 2")
#Test get reverse
d = c.getReverse()
self.assertEqual(str(c), "1 2")
self.assertEqual(str(d), "-2 -1")
#Test fuse
e = c.fuse(d)
self.assertEqual(str(c), "1 2")
self.assertEqual(str(d), "-2 -1")
self.assertEqual(str(e), "1 2 -2 -1")
#Test fuse of null chromosome
e = e.fuse(Chromosome())
self.assertEquals(e.getOrderedElements(), [1, 2, -2, -1])
self.assertEqual(str(e), "1 2 -2 -1")
#Test random breakpoint
for i in xrange(10):
f, g = e.getRandomBreakpoint()
self.assertEqual(str(f.fuse(g)), "1 2 -2 -1")
self.assertEqual(str(d), str(d.clone()))
def testChromosome(self):
"""Test basic functions of a chromosome.
"""
c = Chromosome()
#Append method
c.append(1)
c.append(2)
#Test string generator
self.assertEquals(c.getOrderedElements(), [ 1, 2 ])
self.assertEqual(str(c), "1 2")
#Test get reverse
d = c.getReverse()
self.assertEqual(str(c), "1 2")
self.assertEqual(str(d), "-2 -1")
#Test fuse
e = c.fuse(d)
self.assertEqual(str(c), "1 2")
self.assertEqual(str(d), "-2 -1")
self.assertEqual(str(e), "1 2 -2 -1")
#Test fuse of null chromosome
e = e.fuse(Chromosome())
self.assertEquals(e.getOrderedElements(), [ 1, 2, -2, -1 ])
self.assertEqual(str(e), "1 2 -2 -1")
#Test random breakpoint
for i in xrange(10):
f, g = e.getRandomBreakpoint()
self.assertEqual(str(f.fuse(g)), "1 2 -2 -1")
self.assertEqual(str(d), str(d.clone()))
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()]))
#Command
command = os.path.join(os.path.split(os.path.abspath(matchingAndOrdering.tests.simulatedGenome.__file__))[0], "testBin", "referenceMedianProblemTest2")
output = popenCatch(command, input)
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