def __init__(self): MATCH_STATE = "MATCH_STATE" GAP_STATEX = "GAP_STATEX" GAP_STATEY = "GAP_STATEY" self.xSeq = None self.ySeq = None self.xStart = None self.yStart = None self.stateMachine = SparseAlign.StateMachine() self.stateMachine.addState(MATCH_STATE, self.match_de, SparseAlign.StateMachine.MATCH) self.stateMachine.addState(GAP_STATEX, self.gap_deX, SparseAlign.StateMachine.GAPX) self.stateMachine.addState(GAP_STATEY, self.gap_deY, SparseAlign.StateMachine.GAPY) self.stateMachine.addTransition(MATCH_STATE, MATCH_STATE, self.transitionFn(MATCH)) self.stateMachine.addTransition(MATCH_STATE, GAP_STATEX, self.transitionFn(GAP_OPEN)) self.stateMachine.addTransition(GAP_STATEX, MATCH_STATE, self.transitionFn(GAP_CLOSE)) self.stateMachine.addTransition(GAP_STATEX, GAP_STATEY, self.transitionFn(GAP_SWITCH)) self.stateMachine.addTransition(MATCH_STATE, GAP_STATEY, self.transitionFn(GAP_OPEN)) self.stateMachine.addTransition(GAP_STATEY, MATCH_STATE, self.transitionFn(GAP_CLOSE)) self.stateMachine.addTransition(GAP_STATEY, GAP_STATEX, self.transitionFn(GAP_SWITCH)) self.startStates = [0, 0, 0] #Maths.NEG_INFINITY, Maths.NEG_INFINITY] self.endStates = self.startStates[:] self.diagTraceBackLimit = 1 global m, gapEmissions m = [math.log(i) for i in m] gapEmissions = [math.log(i) for i in gapEmissions] i = [float(i) for i in open("gapDist", 'r').readlines()] j = sum(i) i = [math.log(k / j) for k in i] self.gapDist = i
def __init__(self): MATCH_STATE = "MATCH_STATE" GAP_STATEX = "GAP_STATEX" GAP_STATEY = "GAP_STATEY" self.xSeq = None self.ySeq = None self.xStart = None self.yStart = None self.stateMachine = SparseAlign.StateMachine() self.stateMachine.addState(MATCH_STATE, self.match_de, SparseAlign.StateMachine.MATCH) self.stateMachine.addState(GAP_STATEX, self.gap_de, SparseAlign.StateMachine.GAPX) self.stateMachine.addState(GAP_STATEY, self.gap_de, SparseAlign.StateMachine.GAPY) self.stateMachine.addTransition(MATCH_STATE, MATCH_STATE, self.transitionFn(MATCH)) self.stateMachine.addTransition(MATCH_STATE, GAP_STATEX, self.transitionFn(0.0)) self.stateMachine.addTransition(GAP_STATEX, MATCH_STATE, self.transitionFn(0.0)) self.stateMachine.addTransition(GAP_STATEX, GAP_STATEY, self.transitionFn(GAP_SWITCH)) self.stateMachine.addTransition(MATCH_STATE, GAP_STATEY, self.transitionFn(0.0)) self.stateMachine.addTransition(GAP_STATEY, MATCH_STATE, self.transitionFn(0.0)) self.stateMachine.addTransition(GAP_STATEY, GAP_STATEX, self.transitionFn(GAP_SWITCH)) self.startStates = [0, 0, 0] #Maths.NEG_INFINITY, Maths.NEG_INFINITY] self.endStates = self.startStates[:] self.diagTraceBackLimit = 1 self.COMBINED = GAP_EMISSIONL + GAP_EXTEND self.COMBINED2 = GAP_EMISSIONL + JUNK_EXTEND
MATCH = 0.9703833696510062 GAP_OPEN = (1.0 - MATCH) / 2 GAP_CLOSE = 1.0 - GAP_EXTEND - GAP_SWITCH GAP_SWITCH = 0.0007315179552849 match_match_t = transitionFn(MATCH) match_gap_t = transitionFn(GAP_OPEN) gap_match_t = transitionFn(GAP_CLOSE) gap_gap_t = transitionFn(GAP_SWITCH) """ end space for parameters """ stateMachine = SparseAlign.StateMachine() stateMachine.addState(MATCH_STATE, de, SparseAlign.StateMachine.MATCH) stateMachine.addState(GAP_STATE, de, SparseAlign.StateMachine.GAP) stateMachine.addTransition(MATCH_STATE, MATCH_STATE, t) stateMachine.addTransition(MATCH_STATE, GAP_STATE, t) stateMachine.addTransition(GAP_STATE, MATCH_STATE, t) stateMachine.addTransition(GAP_STATE, GAP_STATE, t) startStates = [0, Maths.NEG_INFINITY] endStates = startStates[:] def diagBuilder(i, j): raise NotImplementedError("Shouldn't be called")