I would do something like:
filename = "mynumbers.txt"
mynumbers = []
with open(filename) as f:
for line in f:
mynumbers.append([int(n) for n in line.strip().split(',')])
for pair in mynumbers:
try:
x,y = pair[0],pair[1]
# Do Something with x and y
except IndexError:
print "A line in the file doesn't have enough entries."
The with open is recommended in http://docs.python.org/tutorial/inputoutput.html since it makes sure files are closed correctly even if an exception is raised during the processing.