Exemple #1
0
def main(rna):
    n = len(rna)
    Z = partFunInner(rna)
    #  print "%s of length %s with total num str of %s" % (rna,n,Z[(1,n)])
    EL = computeEleft(rna, Z)
    ER = computeEright(rna, Z)
    ERprime = computeERprime(rna, Z, ER)
    FF = computeFF(rna, Z)
    J = computeJ(rna, Z, FF)
    Q = computeQ(rna, Z)
    n = len(rna)
    numberNborsNoShift = numNborsNoShift(rna, Z)
    numberNborsWithShift = Q[(1, n)]
    numStr = Z[(1, n)]
    expNumNborsWithoutShift = numberNborsNoShift / float(numStr)
    expNumNborsWithShift = numberNborsWithShift / float(numStr)
    print "rna\t%s" % rna
    print "Z\t%s" % Z[(1, n)]
    print "Q\t%s" % Q[(1, n)]
    print numberNborsNoShift, numberNborsWithShift, numStr, expNumNborsWithoutShift, expNumNborsWithShift
    if PRINT_OUTPUT:
        for i in range(1, n + 1):
            for j in range(i, n + 1):
                print "%s\t%s\t%s" % (i - 1, j - 1, Q[(i, j)])
        for c in NUCL:
            print("Char is %c" % c)
            print "\tEL\t%s" % EL[(1, n, c)]
            print "\tER\t%s" % ER[(1, n, c)]
            print "\tER1\t%s" % ERprime[(1, n, c)]
            for x in range(4):
                print "\tG(0,%s,%s,%s)=%s" % (n - 1, c, x, J[(1, n, c, x)])
        print "Num nbors without shift: ", numberNborsNoShift
        print "Num nbors with shift: ", (numberNborsWithShift -
                                         numberNborsNoShift)
        print "Num nbors: %s" % numberNborsWithShift
        print "Num structures: ", numStr
        print "Exp num nbors without shift: ", expNumNborsWithoutShift
        print "Exp num nbors with shift: ", expNumNborsWithShift
def main(rna):
  n        = len(rna)
  Z        = partFunInner(rna)
#  print "%s of length %s with total num str of %s" % (rna,n,Z[(1,n)])
  EL       = computeEleft(rna,Z)
  ER       = computeEright(rna,Z)
  ERprime  = computeERprime(rna,Z,ER)
  FF       = computeFF(rna,Z)
  J        = computeJ(rna,Z,FF)
  Q  = computeQ(rna,Z)
  n  = len(rna)
  numberNborsNoShift   = numNborsNoShift(rna,Z)
  numberNborsWithShift = Q[(1,n)]
  numStr               = Z[(1,n)]
  expNumNborsWithoutShift = numberNborsNoShift/float(numStr)
  expNumNborsWithShift    = numberNborsWithShift/float(numStr)
  print "rna\t%s" % rna
  print "Z\t%s" % Z[(1,n)]
  print "Q\t%s" % Q[(1,n)]
  print numberNborsNoShift, numberNborsWithShift, numStr, expNumNborsWithoutShift, expNumNborsWithShift
  if PRINT_OUTPUT: 
    for i in range(1,n+1):
      for j in range(i,n+1):
        print "%s\t%s\t%s" % (i-1,j-1,Q[(i,j)])
    for c in NUCL:
      print("Char is %c" % c);
      print "\tEL\t%s" % EL[(1,n,c)]
      print "\tER\t%s" % ER[(1,n,c)]
      print "\tER1\t%s" % ERprime[(1,n,c)]
      for x in range(4):
        print "\tG(0,%s,%s,%s)=%s" % (n-1,c,x,J[(1,n,c,x)])
    print "Num nbors without shift: ", numberNborsNoShift
    print "Num nbors with shift: ",    (numberNborsWithShift-numberNborsNoShift)
    print "Num nbors: %s" % numberNborsWithShift
    print "Num structures: ", numStr
    print "Exp num nbors without shift: ", expNumNborsWithoutShift
    print "Exp num nbors with shift: ",    expNumNborsWithShift
def computeQ(rna,Z):
  FF      = computeFF(rna,Z) 
  J       = computeJ(rna,Z,FF)
  EL      = computeEleft(rna,Z)
  ER      = computeEright(rna,Z)
  ERprime = computeERprime(rna,Z,ER)
  #--------------------------------------------
  #E[(i,j) = sum_S sum_{(x,y)} I[(x,y) external in S]
  # 
  #Ebis[(i,j) = sum_S sum_{(x,y)} I[(x,y) external in S, y<n]
  #
  #Eprime[(i,j) = sum_S sum_{(x,y)} 
  #        I[(x,y) external in S, y <= j-4, j unpaired]
  #EL[(i,j) = sum_S sum_{(x,y)} 
  #        I[(x,y) external in S, x basepairs with rna[n]]
  #ER[(i,j) = sum_S sum_{(x,y)} 
  #        I[(x,y) external in S, y basepairs with rna[n]]
  #ERprime[(i,j) = sum_S sum_{(x,y)} 
  #  I[(x,y) external in S, y basepairs with rna[n], y<=j-4, n unpaired in S]
  Q = {}
  n   = len(rna)
  rna = '$'+rna
  #-------------------------------------------
  #Initialization to zero
  for d in range(n):         #d in [0,n-1]
    for i in range(1,n+1-d): #i in [1,n-d]
      j = i+d
      Q[(i,j)]=0
  #-------------------------------------------
  #Recursions
  for d in range(THETA+1,n):         #d in [4,n-1]
    for i in range(1,n+1-d):         #i in [1,n-d]
      j = i+d
      #Case 1: first term Q(i,j-1)
      Q[(i,j)] = Q[(i,j-1)]
      if PRINT:
        print "\n\n",Q[(i,j-1)], "\tQ(%d,%d)" % (i,j-1)
      #Case 2: second term 2 * sum_k z(i,k-1)*z(k+1,j-1)
      sum = 0
      if basePair(rna[i],rna[j]):
        sum += Z[(i+1,j-1)]
      for k in range(i+1,j-3): #k in [i+1,j-4]
        if basePair(rna[k],rna[j]):
          sum += Z[(i,k-1)]*Z[(k+1,j-1)]
      Q[(i,j)] += 2*sum
      if PRINT:
        text = "\t2 sum_{k=%s}^{%s-4} z(%s,k-1)*z(k+1,%s-1)" 
        print (2*sum),text % (i,j,i,j)
      #Case 3: 2*EL[(i,j-1)]+2*ERprime[(i,j)]
      sum = 2*EL[(i,j-1,rna[j])]+2*ERprime[(i,j,rna[j])]
      Q[(i,j)] += sum
      if PRINT:
        text1 = "%s\t" % sum
        text2 = "2*EL[(%s,%s-1,%s)]+2*ERprime[(%s,%s,%s)]" 
        text2 = text2 % (i,j,rna[j],i,j,rna[j])
        print text1,text2
        text1 = " %s\t" % 2*EL[(i,j-1,rna[j])]
        text2 = "2*EL[(%s,%s-1,%s)]" % (i,j,rna[j])
        print text1,text2
        text1 = " %s\t" % 2*ERprime[(i,j,rna[j])]
        text2 = "2*ERprime[(%s,%s,%s)]" % (i,j,rna[j])
        print text1,text2
      #Case 4: fourth term is sum_{x=2}^{n-4} x*(x-1)*H(1,n,ch,x)
      sum = 0
      for x in range(2,j-i+1-3): #x in [2,j-i+1-4]
        sum += x*(x-1)*J[(i,j,rna[j],x)]
      Q[(i,j)] += sum 
      newsum = 0
      if PRINT:
        text = "\tch\tx\tx-1\tJ(%s,%s,ch,x)\tsum_ch sum_x x(x-1)J(%s,%s,ch,x)"
        print sum,"\tch\tx\tx-1\tJ(1,n,ch,x)\tsum_ch sum_x x(x-1)J(1,n,ch,x)"
        ch = rna[j]
        for x in range(2,j-i+1-3): #x in [2,j-i+1-4]
          print "\t%s\t%s\t%s\t%s = \t%s"%(ch,x,x-1,J[(1,n,ch,x)],x*(x-1)*J[(1,n,ch,x)])
      #Case 5: fifth term  
      #sum_{k=1}^{n-\theta-1} \left( z(k-1) \cdot Q(n-k-1) \right) +
      #\left( Q(k-1) \cdot z(n-k-1) \right)
      #Case 5a: (i,j) paired
      sum = 0
      if basePair(rna[i],rna[j]):
        sum += Q[(i+1,j-1)] 
      for k in range(i+1,j-3): #k in [i+1,j-4]
        if basePair(rna[k],rna[j]):
          sum += (Z[(i,k-1)]*Q[(k+1,j-1)])+(Q[(i,k-1)]*Z[(k+1,j-1)])
      Q[(i,j)] += sum
      if PRINT:
        text = "sum_k (Z[(%s,k-1)]*Q[(k+1,%s-1)])+(Q[(%s,k-1)]*Z[(k+1,%s-1)])"
        text = text % (i,j,i,j)
        print "%s\t%s" % (sum,text)
  return Q         
Exemple #4
0
def computeQ(rna, Z):
    FF = computeFF(rna, Z)
    J = computeJ(rna, Z, FF)
    EL = computeEleft(rna, Z)
    ER = computeEright(rna, Z)
    ERprime = computeERprime(rna, Z, ER)
    #--------------------------------------------
    #E[(i,j) = sum_S sum_{(x,y)} I[(x,y) external in S]
    #
    #Ebis[(i,j) = sum_S sum_{(x,y)} I[(x,y) external in S, y<n]
    #
    #Eprime[(i,j) = sum_S sum_{(x,y)}
    #        I[(x,y) external in S, y <= j-4, j unpaired]
    #EL[(i,j) = sum_S sum_{(x,y)}
    #        I[(x,y) external in S, x basepairs with rna[n]]
    #ER[(i,j) = sum_S sum_{(x,y)}
    #        I[(x,y) external in S, y basepairs with rna[n]]
    #ERprime[(i,j) = sum_S sum_{(x,y)}
    #  I[(x,y) external in S, y basepairs with rna[n], y<=j-4, n unpaired in S]
    Q = {}
    n = len(rna)
    rna = '$' + rna
    #-------------------------------------------
    #Initialization to zero
    for d in range(n):  #d in [0,n-1]
        for i in range(1, n + 1 - d):  #i in [1,n-d]
            j = i + d
            Q[(i, j)] = 0
    #-------------------------------------------
    #Recursions
    for d in range(THETA + 1, n):  #d in [4,n-1]
        for i in range(1, n + 1 - d):  #i in [1,n-d]
            j = i + d
            #Case 1: first term Q(i,j-1)
            Q[(i, j)] = Q[(i, j - 1)]
            if PRINT:
                print "\n\n", Q[(i, j - 1)], "\tQ(%d,%d)" % (i, j - 1)
            #Case 2: second term 2 * sum_k z(i,k-1)*z(k+1,j-1)
            sum = 0
            if basePair(rna[i], rna[j]):
                sum += Z[(i + 1, j - 1)]
            for k in range(i + 1, j - 3):  #k in [i+1,j-4]
                if basePair(rna[k], rna[j]):
                    sum += Z[(i, k - 1)] * Z[(k + 1, j - 1)]
            Q[(i, j)] += 2 * sum
            if PRINT:
                text = "\t2 sum_{k=%s}^{%s-4} z(%s,k-1)*z(k+1,%s-1)"
                print(2 * sum), text % (i, j, i, j)
            #Case 3: 2*EL[(i,j-1)]+2*ERprime[(i,j)]
            sum = 2 * EL[(i, j - 1, rna[j])] + 2 * ERprime[(i, j, rna[j])]
            Q[(i, j)] += sum
            if PRINT:
                text1 = "%s\t" % sum
                text2 = "2*EL[(%s,%s-1,%s)]+2*ERprime[(%s,%s,%s)]"
                text2 = text2 % (i, j, rna[j], i, j, rna[j])
                print text1, text2
                text1 = " %s\t" % 2 * EL[(i, j - 1, rna[j])]
                text2 = "2*EL[(%s,%s-1,%s)]" % (i, j, rna[j])
                print text1, text2
                text1 = " %s\t" % 2 * ERprime[(i, j, rna[j])]
                text2 = "2*ERprime[(%s,%s,%s)]" % (i, j, rna[j])
                print text1, text2
            #Case 4: fourth term is sum_{x=2}^{n-4} x*(x-1)*H(1,n,ch,x)
            sum = 0
            for x in range(2, j - i + 1 - 3):  #x in [2,j-i+1-4]
                sum += x * (x - 1) * J[(i, j, rna[j], x)]
            Q[(i, j)] += sum
            newsum = 0
            if PRINT:
                text = "\tch\tx\tx-1\tJ(%s,%s,ch,x)\tsum_ch sum_x x(x-1)J(%s,%s,ch,x)"
                print sum, "\tch\tx\tx-1\tJ(1,n,ch,x)\tsum_ch sum_x x(x-1)J(1,n,ch,x)"
                ch = rna[j]
                for x in range(2, j - i + 1 - 3):  #x in [2,j-i+1-4]
                    print "\t%s\t%s\t%s\t%s = \t%s" % (ch, x, x - 1, J[
                        (1, n, ch, x)], x * (x - 1) * J[(1, n, ch, x)])
            #Case 5: fifth term
            #sum_{k=1}^{n-\theta-1} \left( z(k-1) \cdot Q(n-k-1) \right) +
            #\left( Q(k-1) \cdot z(n-k-1) \right)
            #Case 5a: (i,j) paired
            sum = 0
            if basePair(rna[i], rna[j]):
                sum += Q[(i + 1, j - 1)]
            for k in range(i + 1, j - 3):  #k in [i+1,j-4]
                if basePair(rna[k], rna[j]):
                    sum += (Z[(i, k - 1)] * Q[(k + 1, j - 1)]) + (Q[
                        (i, k - 1)] * Z[(k + 1, j - 1)])
            Q[(i, j)] += sum
            if PRINT:
                text = "sum_k (Z[(%s,k-1)]*Q[(k+1,%s-1)])+(Q[(%s,k-1)]*Z[(k+1,%s-1)])"
                text = text % (i, j, i, j)
                print "%s\t%s" % (sum, text)
    return Q