problems with file I/O while running python 3.2 scripts in windows cmd, but not in IDLE

Question

I am a python noob, and am having problems running programs with open() functions in cmd prompts. The code runs as expected in the python shell with IDLE, but everytime I open it by doubleclicking the icon coresponding to the script( I have .py associated with python), I get errors like

what file test.txt (I entered input)
file 2 atest2.txt (I entered intput)
Traceback (most recent call last):
File "C:\\Users\\Matthew\\Desktop\\file_io\\find_differences_in_files.py", line 3, in <module>
f=open(c,"r") # open c
IOError: [Errno 22] Invalid argument: 'test.txt\\r'

Similar problems occur in multiple similar programs, but here is a sample of code( FYI, this code finds the first difference in two .txt files) that worked in IDLE but not in cmd. Anybody have any clue what is going wrong?

c=input("what file") # get file 1  
d=input("file 2") # get file 2  
f=open(c,"r") # open c   
g=open(d,"r") # open d  
p=f.readlines() # get every line of f   
q=g.readlines()   
i=0  
while i<len(p) and i<len(q):  
    if p[i]!=q[i]:   
        break # stop counting up  
    i+=1  
x=p[i] # store different line  
y=q[i] # store different line  
j=0  
while j<len(x) or i<len(y):       
    if x[j]!=y[j]:   
        break # stop counting up  
    j+=1  
print("The difference is in line %s column %s" % (i+1,j+1))  
c=input("press enter")

Answer 1

You're not handling end-of-line characters correctly, and IDLE gives you the end-of-line in one format, while the cmd.exe sends another.

I suggest stripping whitespace from both ends of the input in this case.