Splitting string in for loop in python

Question

I'm trying to iterate over a list of rows in a table and do modify a string in one of the columns:

# python 2.7
import csv
import re

with open('root_diff.txt', 'rU') as dmr:
    coordinates_tsv = csv.reader(dmr, delimiter='\t')
    coordinates_list = [row for row in coordinates_tsv]

    for row in coordinates_list:
        cut = re.split(':|-|r', row[3])
        print cut[1]

But I get the following error: IndexError: list index out of range

The string in row[3] looks something like this: chr1:594572-598657. I want to split it so it looks like this: ['ch', '1', '594572', '598657'], and do something with the second and third numbers.

You do not need to create coordinates_list; just loop directly over coordinates_tsv: for row in coordinates_tsv. — Martijn Pieters
– Martijn Pieters, Commented Oct 23, 2013 at 10:26
What line throws the exception? Can you include the full traceback please? — Martijn Pieters
– Martijn Pieters, Commented Oct 23, 2013 at 10:27
Thanks, seems obvious now! Although that wasn't the cause of the error I'm getting — TimStuart
– TimStuart, Commented Oct 23, 2013 at 10:28
That is why I posted that as a comment, not an answer. Without the traceback, I can only guess which one of the two lines is the problem here. — Martijn Pieters
– Martijn Pieters, Commented Oct 23, 2013 at 10:29
Do you have any blank lines in the file? Or a rows that doesn't have 4th column? If row[3] doesn't match your pattern, you won't get an error - I suspect this is your actual problem. — Burhan Khalid
– Burhan Khalid, Commented Oct 23, 2013 at 10:31

Martijn Pieters · Accepted Answer · 2013-10-23 10:37:58Z

2

There must be at least one value for row[3] that doesn't contain any of the characters to split on.

To debug, catch the IndexError and print cut and / or row[3] to see what is going on:

try:
    print cut[1]
except IndexError:
    print '-- unexpected input --', row[3]

If this is the header, skip it with next():

with open('root_diff.txt', 'rU') as dmr:
    coordinates_tsv = csv.reader(dmr, delimiter='\t')

    next(coordinates_tsv, None)  # skip first row, the header

    for row in coordinates_tsv:

Note that in theory, it could also still be the previous line that is throwing this exception; you didn't share the traceback in your post. A blank line or a line with fewer columns would lead to an IndexError for row[3]. A blank line gives an empty list, for example.

edited Oct 23, 2013 at 10:37

answered Oct 23, 2013 at 10:32

Martijn Pieters

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1 Comment

TimStuart Over a year ago

There is a header, I deleted it & it seems to have fixed the problem. Thanks!

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