CODEWITHSUNDEEP
python
Yvonne Gong
Yvonne Gong

Reputation: 9

IndexError: list index out of range, but each string can be printed out

I am writing a script to pool lines from fileA when its first two columns are the same as fileB. The fileA is a txt file with three column separated by tab, and fileB is a txt file with two column separated by tab. But it keeps showing error as following: "site=a[0]+’\t’+a[1] IndexError: list index out of range" But I can print a[0], a[1], a[2] and site.

Here is my code:

fileB=open('AtoG_mock.txt').readlines()
fileA=open('depth_ice.txt').readlines()
outfile=open('AtoG_depth_ice.txt','w')
dict1={}

for line in fileA:
    a=line.strip().split('\t')
    site = a[0]+' '+a[1]
    if site not in dict1:
        dict1[site]=a[2]

for line in fileB:
    b=line.strip().split('\t')
    site=b[0]+' '+b[1]
    if site in dict1:
        outfile.write(b[0]+'\t'+b[1]+'\t'+dict1[site]+'\n')

outfile.close()

I would appreciate any help!

Upvotes: 0

Views: 96

Answers (2)

Leighton
Leighton

Reputation: 1036

I've encountered this sometimes, blank lines for most of time. You may want to check before parsing.

if line == "": pass

The other possibility is missing data.

if len(a) != 3: print a

Upvotes: 0

Tim Pietzcker
Tim Pietzcker

Reputation: 336198

We can't give you a definitive answer because we don't have access to your data files, but you can easily debug this by wrapping the problematic line in a try/except block:

try:
    site = a[0]+' '+a[1]
except IndexError:
    print("Error: a is", a)
    raise

Most probably there's an empty line somewhere, often the last line.

Upvotes: 2

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