Wsrtjtyk

I want to count the number of bases in a DNA sequence, return the counts of each type of base in the sequence, and also print out a two column table where the first column is the base and the second column is the associated base count. I can get the function to return the base count but I am not sure how to print the table. I would like to do this analysis with base python functions although I assume it would be easier to do with some python module.

Code:

 def base_counter(DNA):

    A = 0

    T = 0

    G = 0

    C = 0

    for base in DNA:

        if base == "A":

            A = A + 1

        elif base == "T":

            T = T + 1

        elif base == "G":

            G = G + 1

        elif base == "C":

            C = C + 1

        else:

            pass

    return A,T,G,C

Parameter input:

dna="AAGCTACGTGGGTGACTTT"

Function call:

counts=base_counter(dna)

print(counts)

Output:

(4, 6, 6, 3)

Desired output:

print(counts)

  A   4

  T   6

  G   6

  C   3

and

counts

(4, 6, 6, 3)

from within the function:

out_str="A    "+str(A)+"n"+

      "T    "+str(T)+"n"+

      "G    "+str(G)+"n"+

      "C    "+str(C)

return out_str

now you can call and print it and it will be printed in your desired format:

result=base_counter(DNA)

print(result)

for OP's request full code:

def base_counter(DNA):

    A = 0

    T = 0

    G = 0

    C = 0

    for base in DNA:

        if base == "A":

            A = A + 1

        elif base == "T":

            T = T + 1

        elif base == "G":

            G = G + 1

        elif base == "C":

            C = C + 1

    out_str = "A    " + str(A) + "n"+

    "T    " + str(T) + "n"+

    "G    " + str(G) + "n"+

    "C    " + str(C)

    return out_str



base=base_counter("AAGCTACGTGGGTGACTTT")

print(base)

output:

A    4

T    6

G    6

C    3

You can use collections.Counter to count the bases and pandas to set the data in a column-wise manner. Here is an example

from collections import Counter

import pandas as pd



# Count the bases

dna="AAGCTACGTGGGTGACTTT"

count = Counter(dna)

tup = ()

for _, value in sorted(count.items()):

  tup += (value,)

print(tup  # Outputs (4, 3, 6, 6)



# Set it in a pandas dataframe

df = pd.DataFrame(list(dict(count).items()), columns=['Base', 'Count'])

print(df.to_string(index=False))

# Output

# Base  Count

#   A      4

#   G      6

#   C      3

#   T      6

1) you have a bug - your return is indented one extra tab to the right

2) use a dict:

def base_counter(DNA):

    dna_dict = {

        "A": 0,

        "T": 0,

        "G": 0,

        "C": 0,

    }

    for base in DNA:

        if base == "A":

            dna_dict["A"] += 1

        elif base == "T":

            dna_dict["T"] += 1

        elif base == "G":

            dna_dict["G"] += 1

        elif base == "C":

            dna_dict["C"] += 1

    return dna_dict





dna = "AAGCTACGTGGGTGACTTT"



counts = base_counter(dna)

for base, count in counts.items():

    print(base, count)

but if you have to keep the function as is:

def base_counter(DNA):

    A = 0

    T = 0

    G = 0

    C = 0

    for base in DNA:

        if base == "A":

            A = A + 1

        elif base == "T":

            T = T + 1

        elif base == "G":

            G = G + 1

        elif base == "C":

            C = C + 1

    return A,T,G,C





dna = "AAGCTACGTGGGTGACTTT"



counts = base_counter(dna)

for base, count in zip("ATGC", counts):

    print(base, count)

you can make another function for printing the results:

def print_bases(bases):

print("A    "+str(bases[0])+"n"

  "T    "+str(bases[1])+"n"

  "G    "+str(bases[2])+"n"

  "C    "+str(bases[3]))

print_bases(counts)