I have a python function that randomize a dictionary representing a position specific scoring matrix.
for example:
mat = {
'A' : [ 0.53, 0.66, 0.67, 0.05, 0.01, 0.86, 0.03, 0.97, 0.33, 0.41, 0.26 ]
'C' : [ 0.14, 0.04, 0.13, 0.92, 0.99, 0.04, 0.94, 0.00, 0.07, 0.23, 0.35 ]
'T' : [ 0.25, 0.07, 0.01, 0.01, 0.00, 0.04, 0.00, 0.03, 0.06, 0.12, 0.14 ]
'G' : [ 0.08, 0.23, 0.20, 0.02, 0.00, 0.06, 0.04, 0.00, 0.54, 0.24, 0.25 ]
}
The scambling function:
def scramble_matrix(matrix, iterations):
mat_len = len(matrix["A"])
pos1 = pos2 = 0
for count in range(iterations):
pos1,pos2 = random.sample(range(mat_len), 2)
#suffle the matrix:
for nuc in matrix.keys():
matrix[nuc][pos1],matrix[nuc][pos2] = matrix[nuc][pos2],matrix[nuc][pos1]
return matrix
def print_matrix(matrix):
for nuc in matrix.keys():
print nuc+"[",
for count in matrix[nuc]:
print "%.2f"%count,
print "]"
now to the problem...
When I try to scramble a matrix directly, It's works fine:
print_matrix(mat)
print ""
print_matrix(scramble_matrix(mat,10))
gives:
A[ 0.53 0.66 0.67 0.05 0.01 0.86 0.03 0.97 0.33 0.41 0.26 ]
C[ 0.14 0.04 0.13 0.92 0.99 0.04 0.94 0.00 0.07 0.23 0.35 ]
T[ 0.25 0.07 0.01 0.01 0.00 0.04 0.00 0.03 0.06 0.12 0.14 ]
G[ 0.08 0.23 0.20 0.02 0.00 0.06 0.04 0.00 0.54 0.24 0.25 ]
A[ 0.41 0.97 0.03 0.86 0.53 0.66 0.33.05 0.67 0.26 0.01 ]
C[ 0.23 0.00 0.94 0.04 0.14 0.04 0.07 0.92 0.13 0.35 0.99 ]
T[ 0.12 0.03 0.00 0.04 0.25 0.07 0.06 0.01 0.01 0.14 0.00 ]
G[ 0.24 0.00 0.04 0.06 0.08 0.23 0.54 0.02 0.20 0.25 0.00 ]
but when I try to assign this scrambling to a list , it does not work!!! ...
print_matrix(mat)
s=[]
for x in range(3):
s.append(scramble_matrix(mat,10))
for matrix in s:
print ""
print_matrix(matrix)
result:
A[ 0.53 0.66 0.67 0.05 0.01 0.86 0.03 0.97 0.33 0.41 0.26 ]
C[ 0.14 0.04 0.13 0.92 0.99 0.04 0.94 0.00 0.07 0.23 0.35 ]
T[ 0.25 0.07 0.01 0.01 0.00 0.04 0.00 0.03 0.06 0.12 0.14 ]
G[ 0.08 0.23 0.20 0.02 0.00 0.06 0.04 0.00 0.54 0.24 0.25 ]
A[ 0.01 0.66 0.97 0.67 0.03 0.05 0.33 0.53 0.26 0.41 0.86 ]
C[ 0.99 0.04 0.00 0.13 0.94 0.92 0.07 0.14 0.35 0.23 0.04 ]
T[ 0.00 0.07 0.03 0.01 0.00 0.01 0.06 0.25 0.14 0.12 0.04 ]
G[ 0.00 0.23 0.00 0.20 0.04 0.02 0.54 0.08 0.25 0.24 0.06 ]
A[ 0.01 0.66 0.97 0.67 0.03 0.05 0.33 0.53 0.26 0.41 0.86 ]
C[ 0.99 0.04 0.00 0.13 0.94 0.92 0.07 0.14 0.35 0.23 0.04 ]
T[ 0.00 0.07 0.03 0.01 0.00 0.01 0.06 0.25 0.14 0.12 0.04 ]
G[ 0.00 0.23 0.00 0.20 0.04 0.02 0.54 0.08 0.25 0.24 0.06 ]
A[ 0.01 0.66 0.97 0.67 0.03 0.05 0.33 0.53 0.26 0.41 0.86 ]
C[ 0.99 0.04 0.00 0.13 0.94 0.92 0.07 0.14 0.35 0.23 0.04 ]
T[ 0.00 0.07 0.03 0.01 0.00 0.01 0.06 0.25 0.14 0.12 0.04 ]
G[ 0.00 0.23 0.00 0.20 0.04 0.02 0.54 0.08 0.25 0.24 0.06 ]
What is the problem???
Why the scrambling do not work after the first time, and all the list filled with the same matrix?!
