Forming and parsing multidimensional lists in python - list

Question

I have the following text file-
http://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt
I need a python code to give me the specific entries of the matrix. I'm using multidimensional lists and would prefer doing it without the numpy library in python. My intent is to form lists within lists where the outer(main) list contains rows of the matrix and the inner list contains the cells of the matrix.
I'm using the following code-
handle=open(fname)
li=[]
matrix=[]
for line in handle:
if not line.startswith('#'):
a=line.split()
for i in a:
li.append(i)
matrix.append(li)
print matrix
However, this just returns a one dimensional list with each element being one cell of the matrix. I'm lost regarding how to fix this. The output should be something of this form-
[['A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', 'B', 'Z', 'X', '*'],
['A', '4', '-1', '-2', '-2', '0', '-1', '-1', '0', '-2', '-1', '-1', '-1', '-1', '-2', '-1', '1', '0', '-3', '-2', '0', '-2', '-1', '0', '-4']]

Answer 1

I think you want to produce a matrix, for example matrix[0][1] refer to a value, right? see following code.
handle=open(fname)
matrix=[]
col={}
idx=0
row={}
idr=0
# get 1st line as column
first_line=0
for line in handle:
if not line.startswith('#'):
if first_line == 0:
first_line=1
# get column header
for i in line.split():
col[i]=idx
idx=idx+1
else:
a = line.split()
x = a.pop(0)
# get row name
row[x]=idr
matrix.append(a)
idr=idr+1
print matrix
print matrix[col['A']][row['A']]
See if this is what you want.

Answer 2

You aren't getting the results you want because you're putting all the values into the same li list. The simplest fix for the issue is simply to move the place you create li into the loop:
handle=open(fname)
matrix=[]
for line in handle:
if not line.startswith('#'):
li=[] # move this line down!
a=line.split()
for i in a:
li.append(i)
matrix.append(li)
print matrix
The inner loop there is a bit silly though. You're adding all the values from one list (a) to another list (li), then throwing away the first list. You should just use the list returned by str.split directly:
handle=open(fname)
matrix=[]
for line in handle:
if not line.startswith('#'):
matrix.append(line.split())
print matrix