I am relatively new to python, and have run into an issue with reading a strangely formatted output file.
The current format of the output file for each line is [(x,y),.....(x,y)] (tuples nested within a list?) and I need to read each line in the file and output a 3 columned file with columns X Y and Flavor where flavor is the i-th component in a defined variable.

--thanks

You're welcome.

Could you post an extract of the input file and an example of what you would like in the output one...

One input (the one with the co-ordinates) each of the lines (5500 in this case, must be able to do for different lengths) is in the format that follows
[(0,1),(1,1),(2,1),(2,2),(1,2),(0,3),(-1,4),(-2,4),(-1,5)]

there is also in the program already defined a variable Prot=HPPHPPHHP

the desired outcome is that the program read through each line in the file and for each line output a different file with the format:
0 1 H
1 1 P
2 1 P
2 2 H
1 2 P
0 3 P
-1 4 H
-2 4 H
-1 5 P

The other important thing is that the program is able to account for the fact that it will be run with files of different length in 3 different ways.
1) Number of sets of co-ordinates
2) Number of co-ordinates in a set
3) Length of Prot (= (2) number of co-ordinates in a set)

you've got an easy way of doing this :

datas="""[(0,1),(1,1),(2,1),(2,2),(1,2),(0,3),(-1,4),(-2,4),(-1,5)]
[(0,1),(1,1),(2,1),(2,2),(1,2),(0,3),(-1,4),(-2,4),(-1,5)]
[(0,1),(1,1),(2,1),(2,2),(1,2),(0,3),(-1,4),(-2,4),(-1,5)]""".split('\n')
for data in datas:
    exec ("lst=%s" % data)
    Prot='HPPHPPHHP'
    for i, coord in enumerate(lst):
        for elt in coord:
            print elt,
        print Prot[i]

This is to be adapted for your exact need

i see how this could work, but how can i get Data to be from a read in of an existing file. i tried using openfile and then readlines but then when i try to split the data after it has been readlines'ed i get an error 'list' object has no attribute 'split' which i guess means that my file is read in like a list so then how do i make it read like a string

hmmm i used data=open('file','r') and then Data=data.read() and it actually read it as i would expect it to read it.... hmmm

You can also do like this.
This avoids to load the whole file in memory...

for line in file("myfile.txt"):
    exec ("lst=%s" % line.strip())
    Prot='HPPHPPHHP'
    for i, coord in enumerate(lst):
        for elt in coord:
            print elt,
        print Prot[i]