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Eingabe Datei:
#A, B, D
C, A, A
A, C, C
A, C, G
T, A, A
T, A, T
T, A, X

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Zwischen schirtt:
#A, B, D   A/B B/D A/D
C, A, A        +1
A, C, C        +1        
A, C, G        
T, A, A        +1
T, A, T            +1 
T, A, X        
A, A, T    +1

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Ergebnis:
A/B = 1
B/D = 3
A/D = 1      

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AB = BD = AD = 0
for line in open("../test/input.txt"):
  if line[0] != "#":
    print line.rstrip().split(',')

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>>> spam = """CAA
... ACC    
... ACG       
... TAA
... TAT
... TAX       
... AAT""".splitlines()
>>> def eggs(x):
...     if "X" in x:
...         return None
...     for (i, u), (j, v) in itertools.combinations(enumerate(x), 2):
...         if u == v:
...             return (i, j)
... 
>>> map(eggs, spam)
[(1, 2), (1, 2), (3, 4), (1, 2), (0, 2), None, (0, 1)]

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with open("data") as f:
    first, second, third = map(str.strip, f.readline()[1:].split(",", 3))
    first_with_second = "%s/%s" % (first, second)
    second_with_third = "%s/%s" % (second, third)
    first_with_third = "%s/%s" % (first, third)
    counter = {
        first_with_second : 0,
        second_with_third : 0,
        first_with_third : 0,
        }
    for line in f:
        if line.startswith("#"):
            continue
        first, second, third = map(str.strip, line.split(",", 3))
        if "X" in (first, second, third):
            continue
        elif first == second:
            counter[first_with_second] += 1
        elif first == third:
            counter[first_with_third] += 1
        elif second == third:
            counter[second_with_third] += 1