def main():
count=1
outputList=[]
globalVariables.rawScoreMatrix = pickle.load(open(globalVariables.scoreMatrixFile,"rb"))
globalVariables.states = pickle.load(open(globalVariables.statesFile,"rb"))
globalVariables.timedStates = pickle.load(open(globalVariables.timedStatesFile,"rb"))
# print(globalVariables.rawScoreMatrix)
# print(globalVariables.states)
# print(globalVariables.timedStates)
with open(globalVariables.inputcsv, 'r') as csvfile:
reader = csv.DictReader(csvfile)
names=reader.fieldnames
for row in reader:
# Assuming that the sequences will be in the first two rows
# Compute probabilities with sequence 1 and reverse of sequence 2
seq1=row[names[0]]
seq2=row[names[1]]
scoreMatrix, startPos = score.initScoreMatrix(seq1,seq2)
alinedOne, alinedTwo = score.traceback(scoreMatrix, startPos, seq1,seq2)
alignmentString=score.alignment_string(alinedOne,alinedTwo)
place=globalVariables.reverseEndIndex-globalVariables.reverseStartIndex-1
stateNeeded=state.getState(alinedOne[::-1][place],alinedTwo[::-1][place])
print(count)
print(alinedOne)
print(alignmentString)
print(alinedTwo)
print()
outputList.append(str(count)+","+stateNeeded+","+str(globalVariables.timedStates[place][stateNeeded]['probability']))
count+=1
print()
for line in outputList:
print(line)
def doStuff(seq1,seq2):
# Initialize the scoring matrix.
scoreMatrix, startPos = score.initScoreMatrix(seq1,seq2)
oneAligned, twoAligned = score.traceback(scoreMatrix, startPos, seq1,seq2)
assert len(oneAligned) == len(twoAligned), 'aligned strings are not the same size'
# print(oneAligned)
# print(twoAligned)
state.initStates()
state.initProbabilities(oneAligned,twoAligned)
def doStuff(seq1, seq2):
# Initialize the scoring matrix.
scoreMatrix, startPos = score.initScoreMatrix(seq1, seq2)
oneAligned, twoAligned = score.traceback(scoreMatrix, startPos, seq1, seq2)
assert len(oneAligned) == len(
twoAligned), 'aligned strings are not the same size'
# print(oneAligned)
# print(twoAligned)
state.initStates()
state.initProbabilities(oneAligned, twoAligned)
def main():
count = 1
outputList = []
globalVariables.rawScoreMatrix = pickle.load(
open(globalVariables.scoreMatrixFile, "rb"))
globalVariables.states = pickle.load(open(globalVariables.statesFile,
"rb"))
globalVariables.timedStates = pickle.load(
open(globalVariables.timedStatesFile, "rb"))
# print(globalVariables.rawScoreMatrix)
# print(globalVariables.states)
# print(globalVariables.timedStates)
with open(globalVariables.inputcsv, 'r') as csvfile:
reader = csv.DictReader(csvfile)
names = reader.fieldnames
for row in reader:
# Assuming that the sequences will be in the first two rows
# Compute probabilities with sequence 1 and reverse of sequence 2
seq1 = row[names[0]]
seq2 = row[names[1]]
scoreMatrix, startPos = score.initScoreMatrix(seq1, seq2)
alinedOne, alinedTwo = score.traceback(scoreMatrix, startPos, seq1,
seq2)
alignmentString = score.alignment_string(alinedOne, alinedTwo)
place = globalVariables.reverseEndIndex - globalVariables.reverseStartIndex - 1
stateNeeded = state.getState(alinedOne[::-1][place],
alinedTwo[::-1][place])
print(count)
print(alinedOne)
print(alignmentString)
print(alinedTwo)
print()
outputList.append(
str(count) + "," + stateNeeded + "," +
str(globalVariables.timedStates[place][stateNeeded]
['probability']))
count += 1
print()
for line in outputList:
print(line)