Forming and parsing multidimensional lists in python

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']]

Ronald Poon · Accepted Answer · 2016-02-26 08:38:09Z

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.

edited Feb 26, 2016 at 8:38

answered Feb 26, 2016 at 8:16

Ronald Poon

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1 Comment

Mridul Garg Over a year ago

This is exactly what I wanted. Thanks a lot @Ronald

Blckknght · Accepted Answer · 2016-02-26 08:02:27Z

0

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

edited Feb 26, 2016 at 8:02

answered Feb 26, 2016 at 7:06

Blckknght

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4 Comments

Mridul Garg Over a year ago

This is just giving me a ton of garbage output. My intent of using the inner loop is that the first list should contain cell-wise elements and the second list should be a list of these cell-wise elements for each row.

Blckknght Over a year ago

I guess I don't understand what you want. Can you edit the question to show the desired output?

Mridul Garg Over a year ago

Does this make the question any clearer? @Blckknght

Blckknght Over a year ago

The second version of my code had a typo (missing () at the end of line.split). If you fix that, does it give you the output you expect?

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