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
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