CODEWITHSUNDEEP
python
Paolo Lorenzini
Paolo Lorenzini

Reputation: 725

comparing each sequence created in the loop to the previous

I have created a function in python which randomly generates nucleotide sequence:

import random
selection60 = {"A":20, "T":20, "G":30, "C":30}
sseq60=[]
for k in selection60:
    sseq60 = sseq60 + [k] * int(selection60[k])
    random.shuffle(sseq60)
for i in range(100):
            random.shuffle(sseq60)
def generateSequence(self, length):
    length = int(length)
    sequence = ""
    while len(sequence) < length:
        sequence="".join(random.sample(self, length))
    return sequence[:length]

Now, I would like to check that while I apply this function, if a newly created sequence has a similarity of > 10% to the previous sequences, the sequence is eliminated and a new one is created: I wrote something like this:

    lst60=[]
    newSeq=[]
    for i in range(5):
        while max_identity < 10:
            newSeq=generateSequence(sseq60,100)
            identity[i] = [newSeq[i] == newSeq[i] for i in range(len(newSeq[i]))]
max_identity[I]=100*sum(identity[i]/length(identity[i])
                lst60.append(newSeq)
                print(len(lst60))

However, it seems I get an empty list

Upvotes: 1

Views: 57

Answers (1)

DeGo
DeGo

Reputation: 791

You have to use a nested for loop if you want to compare ith sequence with jth sequence for all 1 <= j < i.

Further, I created a separate getSimilarity function for easier code readability. Pass it an old and new sequence to get the similarity.

def getSimilarity(old_seq, new_seq):
    similarity = [old_seq[i] == new_seq[i] for i in range(len(new_seq))]
    return 100*sum(similarity)/len(similarity)

lst60=[generateSequence(sseq60,100)]
for i in range(1,5):
    newSeq = ""
    max_identity = 0
    while True:
        newSeq = generateSequence(sseq60,100)
        for j in range(0,i):
            max_identity = max(max_identity, getSimilarity(lst60[j], newSeq))
        if max_identity < 10:
            break
    lst60.append(newSeq)
    print(len(lst60))

Upvotes: 1

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