Example #1
0
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
Example #2
0
    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 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 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()))
Example #5
0
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 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