A python random function acts differently when assigned to a list or called directly

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[开发者_JAVA百科 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?!

Your scrambling function is modifying the existing matrix, it is not creating a new one.

You create a matrix, scramble it and add it to a list. Then you scramble it again and add it again to the list. Both elements of the list contain now the same matrix object, which got scrambled twice.

You are shuffling the same matrix in-place for 3 times. But you really want to shuffle 3 copies of original matrix. So you should do:

from copy import deepcopy

print_matrix(mat)
s=[]
for x in range(3):
     s.append(scramble_matrix(deepcopy(mat),10))  # note the deepcopy()
for matrix in s:
     print ""
     print_matrix(matrix)