Question

I wrote a script to reformat a tab-delimited matrix (with header) into a “long format”. See example below. It performs the task correctly but it seems to get stuck in an endless loop…

Example of input:

WHO   THING1    THING2
me    me1       me2
you   you1      you2

Desired output:

me    THING1    me1
me    THING2    me2
you   THING1    you1
you   THING2    you2

Here is the code:

import csv
matrix_file = open('path')
matrix_reader = csv.reader(matrix_file, delimiter="\t")


j = 1
while j:
    matrix_file.seek(0)
    rownum = 0
    for i in matrix_reader:
        rownum+=1
        if j == int(len(i)):
            j = False
        elif rownum ==1:
            header = i[j]
        else:
           print i[0], "\t",header, "\t",i[j]
    j +=1

I think it has to do with my exit command (j = False). Any ideas?

edit: Thanks for suggestions. I think a typo in my initial posting led to some confusion, sorry about that For now I have employed a simple solution:

valid = True
while valid:
matrix_file.seek(0)
rownum = 0
for i in matrix_reader:
    rownum+=1
    if j == int(len(i)):
        valid = False

    etc, etc, etc...

Answer 1

j+=1 is outside the while loop as senderle’s answer says.

other improvements can be:

1. int(len(i)) ,just use len(i) ,as len() always returns a int so no need of int() around
   it
2. use for rownum,i in enumerate(matrix_reader): so now there’s no
   need of handling an extra variable rownum, it’ll be incremented by
   itself.

EDIT: A working version of your code, I don’t think there’s a need of while here, the for loop is sufficient.

import csv
matrix_file = open('data1.csv')
matrix_reader = csv.reader(matrix_file, delimiter="\t")
header=matrix_reader.next()[0].split() #now header is ['WHO', 'THING1', 'THING2']

for i in matrix_reader:
        line=i[0].split()
        print line[0], "\t",header[1], "\t",line[1]
        print line[0], "\t",header[2], "\t",line[2]