Comparing the similarity of nested lists

Question

I have a list of 3 lists that each have 1 list inside each of them.

data_set = [
    ['AB12345',['T','T','C','C','A','C','A','G','C','T','T','T','T','C']],
    ['AB12346',['T','T','C','C','A','C','C','G','C','T','C','T','T','C']],
    ['AB12347',['T','G','C','C','A','C','G','G','C','T','T','C','T','C']]
]

I have a compare method that will give me the similarities of the list which contains the characters, not the id.

def compare(_from, _to):
    similarity = 0
    length = len(_from)
    if len(_from) != len(_to):
        raise Exception("Cannot be compared due to different length.")
    for i in range(length):
        if _from[i] == _to[i]:
            similarity += 1
    return similarity / length * 100

compare(data_set[0][1], data_set[1][1])

By using the compare method, i used a for loop to compare the "a" list with other lists as in "a" compare to "a", "a" compare to "b", and "a" compare to "c".

for i in range(len(data_set)):
    data_set[i].append(compare(data_set[0][1], data_set[i][1]))
    print(round(data_set[i][2], 2), end=", ")

But after finish comparing the 1st list with other lists and itself, how do i loop to the 2nd list and 3rd list and continue compare with other lists again to get their similarities? Like, ( "b" compare to "a", "b" compare to "b" and "b" compare to "c" ) and ( "c" compare to "a", "c" compare to "b" and "c" compare to "c" ).

Answer 1

Just use a second nested loop like that

for i in range(len(data_set)):
    for j in range(len(data_set)):
        data_set[i].append(compare(data_set[j][1], data_set[i][1]))
        print(round(data_set[i][2], 2), end=", ")

Answer 2

For future reference, it's better to include your input lists (a,b,c) in your code instead of using a screen shot to save people having to type out the whole lists. I used some shorter versions for testing.

You could do something like the following to iterate through both lists and compare the results. This is neater than using for i in range(len(data_set)):

# Make some test data
a= ["ID_A", ['T', 'G', 'A']]
b= ["ID_B", ['T', 'C', 'A']]
c= ["ID_C", ['C', 'A', 'A']]

data = [a,b,c]

# entry1 takes each of the values a,b,c in order, and entry2 will do the same,
# so you'll have all possible combinations.
for entry1 in data:
    for entry2 in data:
        score = compare(entry1[1], entry2[1])
        print("Compare ", entry1[0], " to ", entry2[0], "Score :", round(score))

Output:

Compare  ID_A  to  ID_A  Score : 100
Compare  ID_A  to  ID_B  Score : 67
Compare  ID_A  to  ID_C  Score : 33
Compare  ID_B  to  ID_A  Score : 67
Compare  ID_B  to  ID_B  Score : 100
Compare  ID_B  to  ID_C  Score : 33
Compare  ID_C  to  ID_A  Score : 33
Compare  ID_C  to  ID_B  Score : 33
Compare  ID_C  to  ID_C  Score : 100

You're probably better off storing the scores in a different array than the one you're keeping your lists in.

Answer 3

You could also use itertools.combinations to compare all of your sublists. Also, in your compare() function you may want to consider returning a value that indicates sublists are not comparable rather than raising an exception so that you don't short circuit your loop prematurely when comparing a larger set of sublists.

Following is an example (also includes a slightly simpler version of your compare() function that returns -1 when lists are not comparable due to length, but does not perform the comparison of a list against itself since the return value will always be 100 in that situation and seems to be a performance waste).

import itertools

data_set = [
    ['AB12345',['T','T','C','C','A','C','A','G','C','T','T','T','T','C']],
    ['AB12346',['T','T','C','C','A','C','C','G','C','T','C','T','T','C']],
    ['AB12347',['T','G','C','C','A','C','G','G','C','T','T','C','T','C']]
    ]

def compare(a, b):
    length = len(a) if len(a) == len(b) else 0
    similarity = sum(1 for i in range(length) if a[i] == b[i])
    return similarity / length * 100 if length else -1

for a, b in itertools.combinations(data_set, 2):
    compared = a[0] + ' and ' + b[0]
    result = compare(a[1], b[1])
    print(f'{compared}: {result}')

# OUTPUT
# AB12345 and AB12346: 85.71428571428571
# AB12345 and AB12347: 78.57142857142857
# AB12346 and AB12347: 71.42857142857143