Question

I’m having a problem getting my code to do exactly what I want. I would like to define a function that takes two numbers as the arguments and used the numbers to look at a section of the RNA code which is previously stored as a string.

Then I would like to count all possible base pairs in the section so that ‘a’ and ‘u’ pair and ‘g’ and ‘c’ pair. However there has to be a gap of 3 characters between the pairs and the pairs cannot crossover. e.g. if rna[4] pairs with rna[10], rna[5] cannot pair with rna[12]. however if a pair occurred between 4 and 10 i.e. 5 and 9 that would be ok.

so far I have

def base_pairs(x,y):
return (x=='a' and y=='u' or
    x=='u' and y=='a' or
    x=='c' and y=='g' or
    x=='g' and y=='c' or
    x=='g' and y=='u' or
    x=='u' and y=='g' )

rna = raw_input('Enter RNA sequence: ')
n = len(rna)

def opt(x,y):
    for i in range(x,y-5):
        j = i+4
        if base_pairs(rna[i],rna[j])==1:
            print i,j
            a = i
            b = j
            if b-a > 3:
                if base_pairs(a+1,b-1)==1:
                    print a+1,b-1
                    a = a+1
                    b = b-1
        else:
            j=j+1

for example when I input accguugacgcag I would like to use opt(0,12) and get 0,4 5,11 6,10
currently I only get 0,4

Answer 1

I’ve started on a new version of your function. I’ve incorporated the ideas I mentioned in the comments on your question. In addition, I’ve made the rna string a parameter, but this could be removed fairly easily. This version doesn’t produce the output you asked for, but it might be adaptable to meet your needs. The output on my machine is o,4 and 5,9. I couldn’t figure out why you would prefer 5,11 over 5,9 so I couldn’t change it to give that result.

def is_base_pair(x, y):
    return (x=='a' and y=='u' or
            x=='u' and y=='a' or
            x=='c' and y=='g' or
            x=='g' and y=='c' or
            x=='g' and y=='u' or
            x=='u' and y=='g' )

# start and end are the inclusive range of places in which to look for pairs
def opt(rna, start, end):
    # if the range is too small, give up
    if start + 4 > end:
        return

    # the next left side to try to match
    nextLeft = start

    while nextLeft + 4 <= end:
        # find the right nucleobase to match the one at nextLeft
        #   start looking at the minimal distance and incrementally get bigger
        potentialRight = nextLeft + 4
        while not is_base_pair (rna[nextLeft], rna[potentialRight]) and potentialRight <= end:
            potentialRight += 1

        if is_base_pair (rna[nextLeft], rna[potentialRight]):
            print nextLeft, potentialRight
            # recursively search for pairs between the elements of this pair
            opt(rna, nextLeft + 1, potentialRight - 1)
            nextLeft = potentialRight + 1
        else:
            nextLeft += 1

Let me know if you have any questions on how this works.