I would use a for loop to iterate over the lines in the text file:
for line in my_text:
outputfile.writelines(data_parser(line, reps))
If you want to read the file line-by-line instead of loading the whole thing at the start of the script you could do something like this:
inputfile = open('test.dat')
outputfile = open('test.csv', 'w')
# sample text string, just for demonstration to let you know how the data looks like
# my_text = '"2012-06-23 03:09:13.23",4323584,-1.911224,-0.4657288,-0.1166382,-0.24823,0.256485,"NAN",-0.3489428,-0.130449,-0.2440527,-0.2942413,0.04944348,0.4337797,-1.105218,-1.201882,-0.5962594,-0.586636'
# dictionary definition 0-, 1- etc. are there to parse the date block delimited with dashes, and make sure the negative numbers are not effected
reps = {'"NAN"':'NAN', '"':'', '0-':'0,','1-':'1,','2-':'2,','3-':'3,','4-':'4,','5-':'5,','6-':'6,','7-':'7,','8-':'8,','9-':'9,', ' ':',', ':':',' }
for i in range(4): inputfile.next() # skip first four lines
for line in inputfile:
outputfile.writelines(data_parser(line, reps))
inputfile.close()
outputfile.close()