Python - Convert a matrix to edge list/long form

Question

I have a very large csv file, with a matrix like this:

null,A,B,C

A,0,2,3

B,3,4,2

C,1,2,4

It is always a n*n matrix. The first column and the first row are the names. I want to convert it to a 3 column format (also could be called edge list, long form, etc) like this:

A,A,0

A,B,2

A,C,3

B,A,3

B,B,4

B,C,2

C,A,1

C,B,2

C,C,4

I have used:

row = 0
for line in fin:
    line = line.strip("\n")
    col = 0
    tokens = line.split(",")
    for t in tokens:
        fout.write("\n%s,%s,%s"%(row,col,t))
        col += 1
    row += 1

doesn't work...

Could you please help? Thank you..

mtadd · Accepted Answer · 2013-06-14 15:59:37Z

3

You also need to enumerate the column titles as your print out the individual cells.

For a matrix file mat.csv:

null,A,B,C
A,0,2,3
B,3,4,2
C,1,2,4

The following program:

csv = open("mat.csv")

columns = csv.readline().strip().split(',')[1:]
for line in csv:
    tokens = line.strip().split(',')
    row = tokens[0]
    for column, cell in zip(columns,tokens[1:]):
        print '{},{},{}'.format(row,column,cell)

prints out:

A,A,0
A,B,2
A,C,3
B,A,3
B,B,4
B,C,2
C,A,1
C,B,2
C,C,4

For generating the upper diagonal, you can use the following script:

csv = open("mat.csv")

columns = csv.readline().strip().split(',')[1:]
for i, line in enumerate(csv):
    tokens = line.strip().split(',')
    row = tokens[0]
    for column, cell in zip(columns[i:],tokens[i+1:]):
        print '{},{},{}'.format(row,column,cell)

which results in the output:

A,A,0
A,B,2
A,C,3
B,B,4
B,C,2
C,C,4

edited Jun 14, 2013 at 15:59

answered Jun 14, 2013 at 0:55

mtadd

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1 Comment

Brent Washburne Over a year ago

Instead of col=0, set col=row

Brent Washburne · Accepted Answer · 2013-06-14 00:49:51Z

1

You need to skip the first column in each line:

for t in tokens[1:]:

answered Jun 14, 2013 at 0:49

Brent Washburne

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