I think perhaps you are parsing a CSV file that has embedded newlines in some of the text fields. Further, I suppose that the program that created the file put quotation marks (") around the fields.
That is, I supposed that your text file actually looks like this:
1111,AAAA,aaaa
2222,"BB
BB",bbbb
3333,"CCC
C",cccc
If that is the case, you might want to use code with better CSV support than just line.split(','). Consider this program:
import csv
with open('foo.csv') as fp:
reader = csv.reader(fp)
for row in reader:
print row
Which produces this output:
['1111', 'AAAA', 'aaaa']
['2222', 'BB\nBB', 'bbbb']
['3333', 'CCC\nC', 'cccc']
Notice the five lines (delimited by newline characters) of the CSV file become 3 rows (some with embedded newline characters) in the CSV data structure.