def smax(s1, s2):
a1 = pa.alignment(s1, s1)
a2 = pa.alignment(s2, s2)
return float(a1[2] + a2[2]) / 2
def smax(s1, s2):
a1 = pa.alignment(s1, s1)
a2 = pa.alignment(s2, s2)
return float(a1[2] + a2[2]) / 2
def dij(s_ij, s_rand, s_max):
return -np.log(float(s_ij - s_rand) / (s_max - s_rand))
if __name__ == "__main__":
seqs = [
"GCAAAGC",
"GTAGAATC",
"GCCTG",
"CCATC"
]
for i in range(len(seqs)):
for j in range(i + 1, len(seqs)):
a1, a2, score = pa.alignment(seqs[i], seqs[j])
print str(i+1) + ": " + a1
print str(j+1) + ": " + a2
print "score: " + str(score)
s_max = smax(seqs[i], seqs[j])
print "smax: " + str(s_max)
s_rand = srand(a1, a2)
print "srand: " + str(s_rand)
print "D" + str(i+1) + str(j+1) + ": " +\
str(dij(score, s_rand, s_max)) + "\n"