Myunggyo Lee wrote:
> I'm trying to figure out the reason of error but i couldn't find it.
> first imports short.txt(is attached to this mail)
> and read in dictionary named gpdic1
>
>
> Traceback (most recent call last):
> File "/home/ercsb/test.py", line 11, in <module>
> hgene = lines[1]
> IndexError: list index out of range
> # -*- coding: utf-8 -*-
> import string, os, sys, time, glob
>
> inf2 =open('short.txt','r')
>
> gpdic1={}
> while 1:
> line= inf2.readline()
> if not line: break
Add a print statement here to see the problem:
print "processing", repr(line)
Hint: you have an empty line in your data, so:
>>> lines = "\n"[:-1].split(",")
>>> lines
['']
>>> lines[1]
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
IndexError: list index out of range
A possible fix is to skip empty lines
for line in open("short.txt"):
line = line.strip()
if not line:
continue # line contains only whitespace, move on to the next line
... # your code
> lines = line[:-1].split(',')
>
> hgene = lines[1]
> chr1 = lines[4]
> hgstart = lines[5]
> hgstop = lines[6]
> tgene = lines[7]
> chr2 = lines[10]
> tgstart = lines[11]
> tgstop = lines[12]
Note that the following replaces the data of the previous line; once the
while loop has finished you have lost all data except that taken from the
last line in the file.
> gpdic1["hgene"] = hgene
> gpdic1["chr1"] = chr1
> gpdic1["hgstart"] = hgstart
> gpdic1["hgstop"] = hgstop
> gpdic1["tgene"] = tgene
> gpdic1["chr2"] = chr2
> gpdic1["tgstart"] = tgstart
> gpdic1["tgstop"] = tgstop
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