def test_circuitWithGenes(self):
circuit = makeFullTestCircuit()
self.assertEqual(circuit.printAllPartsWithGeneNames()['TOP'],
['P', 'i', 'T'])
self.assertEqual(circuit.printAllPartsWithGeneNames()['BOTTOM'],
['t', 'P', 'G.3.1', 'i', 't'])
circuit1 = enz.induceCircuit(enzyme1, circuit)
self.assertEqual(circuit1.printAllPartsWithGeneNames()['TOP'],
['P', 't', 'P', 'G.3.1', 'i'])
self.assertEqual(circuit1.printAllPartsWithGeneNames()['BOTTOM'],
['i', 'T', 't'])
circuit2 = enz.induceCircuit(enzyme2, circuit1)
self.assertEqual(circuit2.printAllPartsWithGeneNames()['TOP'],
['P', 'T', 'G.3.1', 'i'])
self.assertEqual(circuit2.printAllPartsWithGeneNames()['BOTTOM'],
['i', 't', 'P', 't'])
circuit3 = enz.induceCircuit(enzyme2, circuit)
self.assertEqual(circuit3.printAllPartsWithGeneNames()['TOP'],
['P', 'i'])
self.assertEqual(circuit3.printAllPartsWithGeneNames()['BOTTOM'],
['G.3.1', 'i', 't'])
circuit4 = enz.induceCircuit(enzyme1, circuit3)
self.assertEqual(circuit4.printAllPartsWithGeneNames()['TOP'],
['P', 'G.3.1', 'i'])
self.assertEqual(circuit4.printAllPartsWithGeneNames()['BOTTOM'],
['i', 't'])
def test_circuit_path2(self):
circuit2 = makeCircuit3State()
##The original circuit
self.assertEqual(circuit2.printCircuit(), [1,'D',2,'[',3,'(',4,'-[',5,'(',6,'-D',7])
##Circuit when exposed to Ara
circuitC = enz.induceCircuit(enzyme1, circuit2)
self.assertEqual(circuitC.printCircuit(), [1,'D',-6,'-(',-5,'[',3,'(',4,'-[',-2,'-D',7])
##Circuit when exposed to ATc after Ara
circuitD = enz.induceCircuit(enzyme2, circuitC)
self.assertEqual(circuitD.printCircuit(), [1,'D',-6,'-(',-3,'-[',5,'(',4,'-[',-2,'-D',7])
def test_circuit_path1(self):
circuit1 = makeCircuit3State()
##The original circuit
self.assertEqual(circuit1.printCircuit(), [1,'D',2,'[',3,'(',4,'-[',5,'(',6,'-D',7])
##Circuit when exposed to ATc
circuitA = enz.induceCircuit(enzyme2, circuit1)
self.assertEqual(circuitA.printCircuit(), [1,'D',2,'[',3,'(',6,'-D',7])
##Curcuit when exposed to Ara after ATc
circuitB = enz.induceCircuit(enzyme1, circuitA)
self.assertEqual(circuitB.printCircuit(), [1,'D',-6,'-(',-3,'-[',-2,'-D',7])
def test_circuitWith3Genes(self):
circuit = make3GeneTestCircuit()
self.assertEqual(circuit.printOnlyExpressed(), ['G.5.1', 'G.7.1'])
circuit1 = enz.induceCircuit(enzyme1, circuit)
self.assertEqual(circuit1.printOnlyExpressed(), ['G.7.1'])
circuit2 = enz.induceCircuit(enzyme2, circuit1)
self.assertEqual(circuit2.printOnlyExpressed(), ['G.7.1', 'G.1.1'])
circuit3 = enz.induceCircuit(enzyme2, circuit)
self.assertEqual(circuit3.printOnlyExpressed(), ['G.5.1'])
circuit4 = enz.induceCircuit(enzyme1, circuit3)
self.assertEqual(circuit4.printOnlyExpressed(), ['G.5.1', 'G.1.1'])
def test_simpleCircuit(self):
##Create the circuit
circuit = makeSimpleCicuit()
self.assertEqual(circuit.printCircuit(), [1,'D',2,'-D',3])
newCircuit = enz.induceCircuit(enzyme1,circuit)
self.assertEqual(newCircuit.printCircuit(), [1,'D',-2,'-D',3])
def test_3StateCircuit(self):
circuit = makeCircuit3State()
self.assertEqual(
circuit.printCircuit(),
[5, 'D', 5, '[', 1, '(', -7, '-[', 5, '(', -10, '-D', -10])
self.assertEqual(circuit.printAllParts()['TOP'], ['G', 'i'])
self.assertEqual(circuit.printAllParts()['BOTTOM'],
['P', 'P', 'T', 'i'])
##Induce the circuit with enzyme1 and validate
circuit1 = enz.induceCircuit(enzyme1, circuit)
self.assertEqual(
circuit1.printCircuit(),
[5, 'D', 10, '-(', -5, '[', 1, '(', -7, '-[', -5, '-D', -10])
self.assertEqual(circuit1.printAllParts()['TOP'], ['P', 'G', 'i'])
self.assertEqual(circuit1.printAllParts()['BOTTOM'], ['P', 'T', 'i'])
##Induce the circuit with enzyme2 and validate
circuit2 = enz.induceCircuit(enzyme2, circuit1)
self.assertEqual(
circuit2.printCircuit(),
[5, 'D', 10, '-(', -1, '-[', 5, '(', -7, '-[', -5, '-D', -10])
self.assertEqual(circuit2.printAllParts()['TOP'], ['P', 'i'])
self.assertEqual(circuit2.printAllParts()['BOTTOM'],
['P', 'T', 'G', 'i'])
##Induce the circuit with enzyme2 and validate that it is correct
circuit3 = enz.induceCircuit(enzyme2, circuit)
self.assertEqual(circuit3.printCircuit(),
[5, 'D', 5, '[', 1, '(', -10, '-D', -10])
self.assertEqual(circuit3.printAllParts()['TOP'], ['G', 'i'])
self.assertEqual(circuit3.printAllParts()['BOTTOM'], ['P', 'P', 'i'])
##Inducde the circuit with enzyme1 and validate it
circuit4 = enz.induceCircuit(enzyme1, circuit3)
self.assertEqual(circuit4.printCircuit(),
[5, 'D', 10, '-(', -1, '-[', -5, '-D', -10])
self.assertEqual(circuit4.printAllParts()['TOP'], ['P', 'i'])
self.assertEqual(circuit4.printAllParts()['BOTTOM'], ['P', 'G', 'i'])
def build5StateCircuit(parts):
##Create the recombination sites
site1 = rs.RecognitionSite('D', 1)
site2 = rs.RecognitionSite('[', 1)
site3 = rs.RecognitionSite('(', 1)
site4 = rs.RecognitionSite('[', -1)
site5 = rs.RecognitionSite('(', 1)
site6 = rs.RecognitionSite('D', -1)
sites = [site1, site2, site3, site4, site5, site6]
##Instantiate the circuit
circuit = gc.GeneticCircuit([])
numberOfParts = len(parts)
for pI in range(numberOfParts):
##p is a number
if parts[pI] < 0:
circuit.addComponent(part.Part(abs(parts[pI]), -1))
else:
circuit.addComponent(part.Part(parts[pI], 1))
##Add the site as long as its not the last part
if (pI + 1 < numberOfParts):
circuit.addComponent(sites[pI])
##Want to return all the induced circuits as well
enzyme1 = enz.Enzyme('ATc')
enzyme1.addSiteToRecognize('(')
enzyme2 = enz.Enzyme('Ara')
enzyme2.addSiteToRecognize('[')
enzyme2.addSiteToRecognize('D')
c1 = circuit
c2 = enz.induceCircuit(enzyme1, c1)
c3 = enz.induceCircuit(enzyme2, c1)
c4 = enz.induceCircuit(enzyme2, c2)
c5 = enz.induceCircuit(enzyme1, c3)
return [c1, c2, c3, c4, c5]
def test_simpleCircuit(self):
##Create the circuit
circuit = makeSimpleCircuit()
self.assertEqual(circuit.printCircuit(), [1, 'D', 2, '-D', 3])
##Check the the expression profile is as expected
self.assertEqual(circuit.printAllParts()['TOP'],
['G', 'i', 'G', 'P', 't', 'P'])
self.assertEqual(circuit.printAllParts()['BOTTOM'], ['T', 'i', 'i'])
self.assertEqual(circuit.printOnlyExpressed(), [])
circuit1 = enz.induceCircuit(enzyme1, circuit)
self.assertEqual(circuit1.printAllParts()['TOP'],
['G', 'i', 'i', 't', 'P'])
self.assertEqual(circuit1.printAllParts()['BOTTOM'],
['T', 'G', 'P', 'i'])
circuit.addComponent(part1_1) circuit.addComponent(site1) circuit.addComponent(part2_1) circuit.addComponent(site2) circuit.addComponent(part3_1) circuit.addComponent(site3) circuit.addComponent(part4_1) circuit.addComponent(site4) circuit.addComponent(part5_1) circuit.addComponent(site5) circuit.addComponent(part6_1) circuit.addComponent(site6) circuit.addComponent(part7_1) c2 = enz.induceCircuit(enzyme1, circuit) c3 = enz.induceCircuit(enzyme2, circuit) c4 = enz.induceCircuit(enzyme2, c2) c5 = enz.induceCircuit(enzyme1, c3) # print circuit.printAllPartsWithGeneNames() # print c2.printAllPartsWithGeneNames() # print c3.printAllPartsWithGeneNames() # print c4.printAllPartsWithGeneNames() # print c5.printAllPartsWithGeneNames() # print circuit.printCircuit(excludeRecombinationSites=True) # print c2.printCircuit(excludeRecombinationSites=True) # print c3.printCircuit(excludeRecombinationSites=True) # print c4.printCircuit(excludeRecombinationSites=True) # print c5.printCircuit(excludeRecombinationSites=True)
def build16StateCircuit(parts,
includeAllCircuits=True,
includeTheseCircuits={},
compareTo=[],
getPromsAndTerms=False):
##Create the recombination sites
##TP901 sites: F,O
##BxbI sites: X, I
##A118 sites: A, B
comparingToLength = len(compareTo)
site1 = rs.RecognitionSite('X', 1)
site2 = rs.RecognitionSite('O', 1)
site3 = rs.RecognitionSite('X', -1)
site4 = rs.RecognitionSite('O', 1)
site5 = rs.RecognitionSite('A', 1)
site6 = rs.RecognitionSite('I', 1)
site7 = rs.RecognitionSite('A', -1)
site8 = rs.RecognitionSite('I', 1)
site9 = rs.RecognitionSite('F', 1)
site10 = rs.RecognitionSite('B', 1)
site11 = rs.RecognitionSite('F', -1)
site12 = rs.RecognitionSite('B', 1)
sites = [
site1, site2, site3, site4, site5, site6, site7, site8, site9, site10,
site11, site12
]
##Instantiate the circuit
circuit = gc.GeneticCircuit([])
numberOfParts = len(parts)
partsWithPromotersInThem = {}
partsWithTerminatorsInThem = {}
allCircuits = [None for i in xrange(16)]
for pI in range(numberOfParts):
##p is a number
addedComp = None
if parts[pI] < 0:
posPartId = abs(parts[pI])
addedComp = circuit.addComponent(part.Part(posPartId, -1))
else:
addedComp = circuit.addComponent(part.Part(parts[pI], 1))
##Attempting to remove redundant circuits
if addedComp.getId() not in part.PARTSWITHOUTPROMOTERS:
partsWithPromotersInThem[addedComp.getPartLocation()] = True
##Using the incomplete array because we are only considering part 4 for
##now as a potential redundant terminator part
if addedComp.getId() in part.PARTSWITHTERMINTAORS_INCOMPLETE:
#if addedComp.getId() in part.PARTSWITHTERMINTAORS:
partsWithTerminatorsInThem[addedComp.getPartLocation()] = True
##Add the site as long as its not the last part
if (pI + 1 < numberOfParts):
circuit.addComponent(sites[pI])
if includeAllCircuits:
##Want to return all the induced circuits as well
enzyme1 = enz.Enzyme('BxbI')
enzyme1.addSiteToRecognize('X')
enzyme1.addSiteToRecognize('I')
enzyme2 = enz.Enzyme('TP901')
enzyme2.addSiteToRecognize('F')
enzyme2.addSiteToRecognize('O')
enzyme3 = enz.Enzyme('A118')
enzyme3.addSiteToRecognize('A')
enzyme3.addSiteToRecognize('B')
c1 = circuit
c2 = enz.induceCircuit(enzyme1, c1)
c3 = enz.induceCircuit(enzyme2, c1)
c4 = enz.induceCircuit(enzyme3, c1)
c5 = enz.induceCircuit(enzyme2, c2)
c6 = enz.induceCircuit(enzyme3, c2)
c7 = enz.induceCircuit(enzyme1, c3)
c8 = enz.induceCircuit(enzyme3, c3)
c9 = enz.induceCircuit(enzyme1, c4)
c10 = enz.induceCircuit(enzyme2, c4)
c11 = enz.induceCircuit(enzyme3, c5)
c12 = enz.induceCircuit(enzyme2, c6)
c13 = enz.induceCircuit(enzyme3, c7)
c14 = enz.induceCircuit(enzyme1, c8)
c15 = enz.induceCircuit(enzyme2, c9)
c16 = enz.induceCircuit(enzyme1, c10)
allCircuits = [
c1, c2, c3, c4, c5, c6, c7, c8, c9, c10, c11, c12, c13, c14, c15,
c16
]
if getPromsAndTerms:
return {
'allCircuits': allCircuits,
'partsWithPromotersInThem': partsWithPromotersInThem,
'partsWithTerminatorsInThem': partsWithTerminatorsInThem
}
else:
return allCircuits
elif len(includeTheseCircuits) > 0:
##Want to return only a subset of the circuits
enzyme1 = enz.Enzyme('BxbI')
enzyme1.addSiteToRecognize('X')
enzyme1.addSiteToRecognize('I')
enzyme2 = enz.Enzyme('TP901')
enzyme2.addSiteToRecognize('F')
enzyme2.addSiteToRecognize('O')
enzyme3 = enz.Enzyme('A118')
enzyme3.addSiteToRecognize('A')
enzyme3.addSiteToRecognize('B')
enzymes = [enzyme1, enzyme2, enzyme3]
parentCircuit = [None, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 5, 6, 7, 8, 9]
inducingEnzyme = [None, 0, 1, 2, 1, 2, 0, 2, 0, 1, 2, 1, 2, 0, 1, 0]
for i in xrange(len(allCircuits)):
if len(includeTheseCircuits) > 0:
if (i + 1) not in includeTheseCircuits:
continue
if i == 0:
if comparingToLength > 0:
if getNumberOfGenesExpressedForCircuit([circuit
]) != compareTo[i]:
return False
allCircuits[0] = circuit
else:
allCircuits[i] = enz.induceCircuit(
enzymes[inducingEnzyme[i]], allCircuits[parentCircuit[i]])
if comparingToLength > 0:
if getNumberOfGenesExpressedForCircuit([allCircuits[i]
]) != compareTo[i]:
return False
return allCircuits
else:
return [circuit]