def make3GeneTestCircuit():
##Create the circuit
circuit = gc.GeneticCircuit([])
component11 = part.Part(1, -1)
component22 = part.Part(14, 1)
component33 = part.Part(2, 1)
component44 = part.Part(1, -1)
component55 = part.Part(5, 1)
component66 = part.Part(5, 1)
component77 = part.Part(14, -1)
circuit.addComponent(component11)
circuit.addComponent(site1)
circuit.addComponent(component22)
circuit.addComponent(site2)
circuit.addComponent(component33)
circuit.addComponent(site3)
circuit.addComponent(component44)
circuit.addComponent(site4)
circuit.addComponent(component55)
circuit.addComponent(site5)
circuit.addComponent(component66)
circuit.addComponent(site6)
circuit.addComponent(component77)
return copy.deepcopy(circuit)
def makeFullTestCircuit():
##Create the circuit
circuit = gc.GeneticCircuit([])
component1 = part.Part(14, 1)
component2 = part.Part(1, -1)
component3 = part.Part(5, 1)
component4 = part.Part(5, 1)
component5 = part.Part(3, -1)
component6 = part.Part(5, 1)
component7 = part.Part(5, 1)
circuit.addComponent(component1)
circuit.addComponent(site1)
circuit.addComponent(component2)
circuit.addComponent(site2)
circuit.addComponent(component3)
circuit.addComponent(site3)
circuit.addComponent(component4)
circuit.addComponent(site4)
circuit.addComponent(component5)
circuit.addComponent(site5)
circuit.addComponent(component6)
circuit.addComponent(site6)
circuit.addComponent(component7)
return copy.deepcopy(circuit)
def makeCircuit3State():
##Create the circuit
circuit = gc.GeneticCircuit([])
##Overwrite the parts in this circuit
part1_1 = part.Part(5, 1)
part2_1 = part.Part(5, 1)
part3_1 = part.Part(1, 1)
part4_1 = part.Part(7, -1)
part5_1 = part.Part(5, 1)
part6_1 = part.Part(10, -1)
part7_1 = part.Part(10, -1)
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)
return copy.deepcopy(circuit)
def __cutCircuit(oldCircuitComponents, cut1, cut2): tempCircuit = gc.GeneticCircuit([]) for i in range(len(oldCircuitComponents)): if cut1 <= i and i < cut2: next else: tempCircuit.addComponent(oldCircuitComponents[i]) return tempCircuit
def makeSimpleCicuit():
circuit = gc.GeneticCircuit([])
circuit.addComponent(part1)
circuit.addComponent(site1)
circuit.addComponent(part2)
circuit.addComponent(site6)
circuit.addComponent(part3)
return copy.deepcopy(circuit)
def buildOneCircuit(parts):
##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))
return [circuit]
def makeCircuit3State():
##Create the circuit
circuit = gc.GeneticCircuit([])
circuit.addComponent(part1)
circuit.addComponent(site1)
circuit.addComponent(part2)
circuit.addComponent(site2)
circuit.addComponent(part3)
circuit.addComponent(site3)
circuit.addComponent(part4)
circuit.addComponent(site4)
circuit.addComponent(part5)
circuit.addComponent(site5)
circuit.addComponent(part6)
circuit.addComponent(site6)
circuit.addComponent(part7)
return copy.deepcopy(circuit)
def induceCircuit(enzyme, geneticcircuit): ##Now iterate through each site that this enzyme recognizes and id the ##genetic circuit contains those sites, then we have to either flip or cut components = geneticcircuit.getComponents() newCircuit = gc.GeneticCircuit(components) for site in enzyme.sitesRecognized: ##Get the cut site locations, which can be different from what they were ##in the original circuit if it's been cut siteLocations = __getCutSiteLocations(enzyme, newCircuit) if site in siteLocations: ##There are cut sites. Check if there are two. Won't worry about other ##Cases for now but should be implemented later on ## ##TODO: handle cases when there are more than 2 cut sites if len(siteLocations[site]) == 2: [cut1, cut2] = siteLocations[site] tempCircuit = __induceWithSingleSite(newCircuit, cut1, cut2) newCircuit = tempCircuit return newCircuit
def __flipCircuit(oldCircuitComponents, flip1, flip2): tempCircuit = gc.GeneticCircuit([]) subComponents = oldCircuitComponents[flip1:flip2+1][:] newSubsComps = [] for element in subComponents: ##Create new element instance so original circuit does not get modified if isinstance(element, part.Part): newElement = part.Part(element.getId(), element.getOrientation(), element.getPartLocation()) else: newElement = rs.RecognitionSite(element.getSymbol(), element.getOrientation()) newElement.flip() newSubsComps.append(newElement) newSubsComps.reverse() for i in range(len(oldCircuitComponents)): if flip1 <= i and i <= flip2: tempCircuit.addComponent(newSubsComps[i-flip1]) else: tempCircuit.addComponent(oldCircuitComponents[i]) return tempCircuit
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 convertFromAsGeneticCircuits(stateNumber, gcElement):
components = gcElement.getComponents()[:]
##Flip components order and return newCircuit
newComponents = convertFrom(stateNumber, components)
return gc.GeneticCircuit(newComponents)
import Part as part
import RecognitionSite as rs
import GeneticCircuit as gc
import Enzyme as enz
##Create the enzymes
enzyme1 = enz.Enzyme('Ara')
enzyme1.addSiteToRecognize('[')
enzyme1.addSiteToRecognize('D')
enzyme2 = enz.Enzyme('ATc')
enzyme2.addSiteToRecognize('(')
circuit = gc.GeneticCircuit([])
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)
##Overwrite the parts in this circuit
part1_1 = part.Part(1, 1)
part2_1 = part.Part(3, 1)
part3_1 = part.Part(5, 1)
part4_1 = part.Part(7, 1)
part5_1 = part.Part(9, 1)
part6_1 = part.Part(11, 1)
part7_1 = part.Part(13, 1)
circuit.addComponent(part1_1)
def subPartArrayExpressionVectorAnalysis_Iso(subPartArray):
configurations = [[0, 1, 2, 3, 4], [0, -2, -1, 3, 4], [0, 1, 4],
[0, -2, -3, 1, 4]]
numberOfGenes = 0
for i in subPartArray:
absI = abs(i)
if absI in geneCount:
numberOfGenes += geneCount[absI]
geneExpressionByState = {}
geneExpressionByStateArray = [{}, {}, {}, {}]
outputsByState = []
##Read through states passed
readThroughCircuitStatesPassed = 0
for ci in xrange(len(configurations)):
config = configurations[ci]
circuit = gc.GeneticCircuit([])
numberOfParts = len(config)
for partLocation in config:
##Create parts to add
pId = subPartArray[abs(partLocation)]
##For the first part, since its a 0
if partLocation == 0 and pId < 0:
circuit.addComponent(part.Part(abs(pId), -1,
abs(partLocation)))
elif partLocation == 0 and pId > 0:
circuit.addComponent(part.Part(abs(pId), 1, abs(partLocation)))
elif (partLocation < 0 and pId > 0) or (partLocation > 0
and pId < 0):
##It is flipped
circuit.addComponent(part.Part(abs(pId), -1,
abs(partLocation)))
else:
circuit.addComponent(part.Part(abs(pId), 1, abs(partLocation)))
partsTopAndBottom = circuit.printAllParts(withLocations=True)
##Read-through check (should never happen for parts with terms)
if len(partsTopAndBottom['TOP']) == 0 or len(
partsTopAndBottom['BOTTOM']) == 0:
return 'READTHROUGH'
else:
readThroughCircuitStatesPassed += 1
if ci == 0:
for ps in partsTopAndBottom['TOP']:
##Get the genes out
if ps[0] == 'G':
if ps != 'G.0.1':
geneExpressionByState[ps] = []
for ps in partsTopAndBottom['BOTTOM']:
##Get the genes out
if ps[0] == 'G':
if ps != 'G.4.1':
geneExpressionByState[ps] = []
expressedGenesInThisState = circuit.printOnlyExpressed(
returnOnlyExpressedGenes=False)
for gene in expressedGenesInThisState['expressedGenes']:
geneExpressionByState[gene].append(ci)
geneExpressionByStateArray[ci][gene] = True
outputsByState.append({
'topRight':
expressedGenesInThisState['topOutputState'],
'bottomLeft':
expressedGenesInThisState['bottomOutputState']
})
# print geneExpressionByState
for gene in geneExpressionByState:
if len(geneExpressionByState[gene]) == 0 or len(
geneExpressionByState[gene]) == 4:
##This part is either unused or always used and should not be included
# print gene
return False
return {
'genesToStates': geneExpressionByState,
'statesToGenes': geneExpressionByStateArray,
'outputs': outputsByState,
'numberOfGenes': numberOfGenes
}
def generatePromoterOutputs(subPartArray, leftOnly=False, rightOnly=False):
##If we see G.0.1 being transcribed, then we know that the output is 1 on the left
#else it's 0 if we see G.4.1 being transcribed, then we know that the output is 1
##on the right else it is 0
configurations = [[0, 1, 2, 3, 4], [0, -2, -1, 3, 4], [0, 1, 4],
[0, -2, -3, 1, 4]]
geneExpressionByState = {}
geneExpressionByStateArray = [{}, {}, {}, {}]
outputsByState = [{}, {}, {}, {}]
for ci in xrange(len(configurations)):
config = configurations[ci]
circuit = gc.GeneticCircuit([])
numberOfParts = len(config)
for partLocation in config:
##Create parts to add
pId = subPartArray[abs(partLocation)]
##For the first part, since its a 0
if partLocation == 0 and pId < 0:
circuit.addComponent(part.Part(abs(pId), -1,
abs(partLocation)))
elif partLocation == 0 and pId > 0:
circuit.addComponent(part.Part(abs(pId), 1, abs(partLocation)))
elif (partLocation < 0 and pId > 0) or (partLocation > 0
and pId < 0):
##It is flipped
circuit.addComponent(part.Part(abs(pId), -1,
abs(partLocation)))
else:
circuit.addComponent(part.Part(abs(pId), 1, abs(partLocation)))
partsTopAndBottom = circuit.printAllParts(withLocations=True)
##Read through check
if len(partsTopAndBottom['TOP']) == 0 or len(
partsTopAndBottom['BOTTOM']) == 0:
return 'READTHROUGH'
if ci == 0:
if not rightOnly:
for ps in partsTopAndBottom['TOP']:
##Get the genes out
if ps[0] == 'G':
geneExpressionByState[ps] = []
if not leftOnly:
for ps in partsTopAndBottom['BOTTOM']:
##Get the genes out
if ps[0] == 'G':
geneExpressionByState[ps] = []
##Check if we should be skip the circuit
shouldSkip = circuit.printAllParts()
if len(shouldSkip['TOP']) == 0 or len(shouldSkip['BOTTOM']) == 0:
# print subPartArray
# print shouldSkip
return 'READTHROUGH'
expressedGenesInThisState = circuit.printOnlyExpressed(
returnOnlyExpressedGenes=False)
outputsByState[ci]['topRight'] = expressedGenesInThisState[
'topOutputState']
outputsByState[ci]['bottomLeft'] = expressedGenesInThisState[
'bottomOutputState']
# print expressedGenesInThisState['expressedPromotersFull']
for gene in expressedGenesInThisState['expressedGenes']:
if gene in geneExpressionByState:
geneExpressionByState[gene].append(ci)
geneExpressionByStateArray[ci][gene] = True
return {
'genesToStates': geneExpressionByState,
'statesToGenes': geneExpressionByStateArray,
'outputs': outputsByState
}
def subCircuitUsedAndUnusedParts(subPartArray, segmentNumber=2):
##The sub array has to be a length 5
# print segmentNumber
##We are going to exluce 4's and 6's from this as well because we want to include these so
##that we know when to replace with one sided genes or promoters
toExclude = set([5])
if segmentNumber == 1:
if abs(subPartArray[4]) in toExclude:
return False
elif segmentNumber == 2:
if abs(subPartArray[0]) in toExclude or abs(
subPartArray[4]) in toExclude:
return False
elif segmentNumber == 3:
if abs(subPartArray[0]) in toExclude:
return False
##We only need to check four possible configurations
configurations = [[0, 1, 2, 3, 4], [0, -2, -1, 3, 4], [0, 1, 4],
[0, -2, -3, 1, 4]]
stateNumberToConfig = [
0,
]
toIgnore = {
'G.0.1': [1, 2, 8],
'P.0.1': [-2, -3],
'P.0.2': [6, -3],
'G.4.1': [-1, -2],
'G.4.2': [8],
'P.4.1': [2, 3, 6],
'T.4': [3, -3]
}
allParts = {}
validPartLetters = set(['P', 'G', 'T'])
##For each config, we build a circuit and analyze it and in the end
##We will determine which components have been used
for ci in xrange(len(configurations)):
config = configurations[ci]
##First have to look at the top
circuit = gc.GeneticCircuit([])
numberOfParts = len(config)
for partLocation in config:
##Create parts to add
pId = subPartArray[abs(partLocation)]
# print pId
# print partLocation
##For the first part, since its a 0
if partLocation == 0 and pId < 0:
circuit.addComponent(part.Part(abs(pId), -1,
abs(partLocation)))
elif partLocation == 0 and pId > 0:
circuit.addComponent(part.Part(abs(pId), 1, abs(partLocation)))
elif (partLocation < 0 and pId > 0) or (partLocation > 0
and pId < 0):
##It is flipped
circuit.addComponent(part.Part(abs(pId), -1,
abs(partLocation)))
else:
circuit.addComponent(part.Part(abs(pId), 1, abs(partLocation)))
##We can get all the parts for this sub circuit in the first config
if ci == 0:
partsTopAndBottom = circuit.printAllParts(withLocations=True)
for p in partsTopAndBottom['TOP']:
if p[0] in validPartLetters:
##Special case for term, where we only add the first two parts of the string
##This is because we are only using bidirectional terms, so we are only
##considering it un unused term if BOTH terms on the bidirectional term
##are unused (do not change the expression of the genes)
if p[0] == 'T':
##Split the part
splitPart = p.split('.')
if abs(subPartArray[int(splitPart[1])]) == 4:
newPartName = str(splitPart[0]) + '.' + str(
splitPart[1])
allParts[newPartName] = False
# elif p[0] == 'P':
# ##Split the part
# ##If one of the parts with a 6 in it is used, then we want to keep this
# ##this circuit
# splitPart = p.split('.')
# if abs(subPartArray[int(splitPart[1])]) == 6:
# newPartName = str(splitPart[0]) + '.' + str(splitPart[1])
# allParts[newPartName] = False
else:
allParts[p] = False
for p in partsTopAndBottom['BOTTOM']:
if p[0] in validPartLetters:
if p[0] == 'T':
##Split the part
splitPart = p.split('.')
if abs(subPartArray[int(splitPart[1])]) == 4:
newPartName = str(splitPart[0]) + '.' + str(
splitPart[1])
allParts[newPartName] = False
##If one of the parts with a 6 in it is used, then we want to keep this
##this circuit
# elif p[0] == 'P':
# ##Split the part
# splitPart = p.split('.')
# if abs(subPartArray[int(splitPart[1])]) == 6:
# newPartName = str(splitPart[0]) + '.' + str(splitPart[1])
# allParts[newPartName] = False
else:
allParts[p] = False
##Now look at the expression of this circuit
# print circuit.printCircuit()
expressionVector = circuit.printOnlyExpressed(
returnOnlyExpressedGenes=False)
# print expressionVector
for k in expressionVector['expressedPromotersFull']:
allParts[k] = True
for k in expressionVector['expressedGenes']:
allParts[k] = True
##Looking at terminators
for k in expressionVector['expressedTerminatorsFull']:
splitTermPart = k.split('.')
newname = str(splitTermPart[0]) + '.' + str(splitTermPart[1])
allParts[newname] = True
# print "Segment num: " + str(segmentNumber) + "," + str(subPartArray)
# print allParts
# print segmentNumber
# print allParts
for k in allParts:
if not allParts[k]:
##We just have to do a quick check that it is not a gene on one of the ends
##which could be used in a dffferent section
if k in toIgnore:
# print 'Looking to ignore: ' + str(k)
splitK = k.split('.')
if subPartArray[int(splitK[1])] in toIgnore[k]:
continue
##Here is where we can figure out all of the circuits that we can skip
##because they have they will have this sub segment (its all of the) circuit ids
##that have this exact subsegment, so just have to check five values
# print 'The one that failed: ' + str(k)
# print k
return True
# print 'Should be false....'
return False
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]
def subPartArrayExpressionVectorAnalysis_NonIso(subPartArray,
readThrough=False):
startStateCombos = [(0, 0), (0, 1), (1, 0), (1, 1)]
configurations = [[0, 1, 2, 3, 4], [0, -2, -1, 3, 4], [0, 1, 4],
[0, -2, -3, 1, 4]]
##We are going to skip designs that have no genes in them because there is an
##extra layer of complication that we have to consider with these.
##This may not be necessary anymore
numberOfGenes = 0
for i in subPartArray:
absI = abs(i)
if absI in geneCount:
numberOfGenes += geneCount[absI]
numberOfNonReadThroughStates = 0
geneExpressionByState = {}
geneExpressionByStateArray = [{}, {}, {}, {}]
outputsByState = [{}, {}, {}, {}]
for ci in xrange(len(configurations)):
config = configurations[ci]
circuit = gc.GeneticCircuit([])
numberOfParts = len(config)
for partLocation in config:
##Create parts to add
pId = subPartArray[abs(partLocation)]
##For the first part, since its a 0
if partLocation == 0 and pId < 0:
circuit.addComponent(part.Part(abs(pId), -1,
abs(partLocation)))
elif partLocation == 0 and pId > 0:
circuit.addComponent(part.Part(abs(pId), 1, abs(partLocation)))
elif (partLocation < 0 and pId > 0) or (partLocation > 0
and pId < 0):
##It is flipped
circuit.addComponent(part.Part(abs(pId), -1,
abs(partLocation)))
else:
circuit.addComponent(part.Part(abs(pId), 1, abs(partLocation)))
partsTopAndBottom = circuit.printAllParts(withLocations=True)
##Read-through check
readThroughCircuit = False
if len(partsTopAndBottom['TOP']) == 0 or len(
partsTopAndBottom['BOTTOM']) == 0:
if not readThrough:
return 'READTHROUGH'
else:
readThroughCircuit = True
##In the case when we only want circuits that have read through
if not readThroughCircuit and readThrough:
numberOfNonReadThroughStates += 1
if numberOfNonReadThroughStates == 4:
return 'NONREADTHROUGH'
if ci == 0:
for ps in partsTopAndBottom['TOP']:
##Get the genes out
if ps[0] == 'G':
# if ps != 'G.0.1':
geneExpressionByState[ps] = [{}, {}, {}, {}]
for ps in partsTopAndBottom['BOTTOM']:
##Get the genes out
if ps[0] == 'G':
# if ps != 'G.4.1':
geneExpressionByState[ps] = [{}, {}, {}, {}]
for reading in startStateCombos:
expressedGenesInThisState = circuit.printOnlyExpressed(
returnOnlyExpressedGenes=False,
topStart=reading[0],
bottomStart=reading[1])
geneExpressionByStateArray[ci][
reading] = expressedGenesInThisState['expressedGenes']
for gene in expressedGenesInThisState['expressedGenes']:
geneExpressionByState[gene][ci][reading] = True
##Have to check this outputs stuff again as I am realizing it doesn't make sense.
##For most of the non-isos, it may be state independent actually, so we do not need
##to worry about the input. TRUE but need the reading for cases with dependencies
##like the read through case
outputsByState[ci][reading] = {
'topRight':
expressedGenesInThisState['topOutputState'],
'bottomLeft':
expressedGenesInThisState['bottomOutputState'],
##For cases when we want to check if the out put state is due to the
##input state
'topStateChanged':
expressedGenesInThisState['topStateChanged'],
'bottomStateChanged':
expressedGenesInThisState['bottomStateChanged']
}
# for sn in geneExpressionByStateArray:
# print sn
return {
'numberOfGenes': numberOfGenes,
'genesToStates': geneExpressionByState,
'statesToGenes': geneExpressionByStateArray,
'outputs': outputsByState
}
