Finding how many times a nucleotide appear in the same position

Question

[ran]

Hello, I'm new to the world of python and im trying to solve a question which I am given a few dna sequences, for example: sequences = ["GAGGTAAACTCTG", "TCCGTAAGTTTTC", "CAGGTTGGAACTC", "ACAGTCAGTTCAC", "TAGGTCATTACAG", "TAGGTACTGATGC"]

I want to know how many times the nucleotide "A" is in the first position [0] of all of those sequences (the answer should be 1 in that case). Im trying to use for loop but don't really know how to move forward. Ill appreciate any help, Thank you!

[hugo.avila]

Hi, It is not a norm but it is a good practice to post an attempted resolution first and then other members try to correct it or suggest another answer. You said you are a python beginner so don't worry about judgments you can post any attempt no matter how bad it went. ;)

[Pierre Lindenbaum]

cross posted: https://stackoverflow.com/questions/67060118/

[cpad0112]

#!/usr/bin/env python3

sequences = ["GAGGTAAACTCTG", "TCCGTAAGTTTTC", "CAGGTTGGAACTC", "ACAGTCAGTTCAC", "TAGGTCATTACAG", "TAGGTACTGATGC"]

def count_first_base(sequences=sequences, base="A"):
    count = [int(i[0] == base) for i in sequences]
    return [count, sum(count)]

print(*count_first_base(), sep="\n")

[0, 0, 0, 1, 0, 0]

1

Answer 1

[Dunois]

Here's a little python function you can work off of:

def count_quer_at_pos_in_seq(seqs, quer = "A"):

    #Initialize a list of zeroes, and make it 
    #as long as the longest input sequence.
    #This will be used to store the counts for the 
    #character counts at each position (along the 
    #length of the sequences).
    out = [0]*max([len(seq) for seq in seqs])

    #For each sequence in the list sequences:
    for seq in seqs:

        #For each position in the current sequence:
        for pos in range(len(seq)):

            #Check if the character at the current position 
            #is identical to the query character supplied by 
            #the user.
            if seq[pos] == quer:
                #If it is, increment the count in the list "out" 
                #by one.
                out[pos] += 1

    #Return out to the calling environment.
    return(out)


#----

#Test run.
sequences = ["GAGGTAAACTCTG", "TCCGTAAGTTTTC", "CAGGTTGGAACTC", "ACAGTCAGTTCAC", "TAGGTCATTACAG", "TAGGTACTGATGC"]
count_quer_at_pos_in_seq(sequences, quer = 'A')

#[1, 4, 1, 0, 0, 3, 4, 1, 1, 3, 0, 2, 0]