help need on file reading and writing in python

[chebude]

I am a bigginer in python and even programming. I want to use python in my thesis for reading and writing large size data. I have a little sample of code which access which runs over the lines and reads each element on a line.

def get_site_only(pat):
    newpat = ""
    for c in pat:
        if c.isalpha():
            newpat +=c
    return newpat

def read_rebase(filename):
    enz_dict={}
    infh= open("rebase.dat")
    for line in infh.xreadlines():
        fields = line.split()
        name = line.split()[0]
        pat = line.split()[2]
        enz_dict[name] = get_site_only(pat)

    infh.close()
    return enz_dict

print read_rebase("rebase.dat")

I get the following error message:

Traceback (most recent call last):
File "D:\Downloads\Python2\trial3.py", line 20, in <module>
print read_rebase("rebase.dat")
File "D:\Downloads\Python2\trial3.py", line 13, in read_rebase
name = line.split()[0]
IndexError: list index out of range

would you please help me with this problem

chebude

[lllllIllIlllI]

Well the problem is that in your text file you may have an empty line and therefore splitting it will give you a list with nothing in it and therefore if you try and acces the variable at location 0 there is nothing there.
A list index out of range means that the list is not large enough to have a value stored at that location.

Hope that clears it up.

[Stefano Mtangoo]

make another function to strip spaces
And then the storm will end!

Paul have made it clear

[chebude]

You are right the problem was the empty spaces below my data raws. After removing the empty spaces it runs very well.

Thank you a lot. It was a big help!

[jlm699]

To avoid this problem in the future you could do this:

def read_rebase(filename):
    enz_dict={}
    infh= open("rebase.dat")
    for line in infh.xreadlines():
        fields = line.split()
        if len(fields) > 2:
            name = line.split()[0]
            pat = line.split()[2]
            enz_dict[name] = get_site_only(pat)

    infh.close()
    return enz_dict

This way you make sure that the number of elements matches the indices that you're requesting.