Count-DNA-Nucleotides

Used for counting the number of all four nucleotides and finding the percentage number of each of them

About the project

This program made are specifically for studies made with genetics and organisms in microbiology such as viruses or bacterias. There are a few features here:

1. Counting the amount of nucleotides (in a specific sequence)
2. counting the percentage of each nucleotide

You can count all nucleotides in DNA and RNA.

How does this work

Genetic sequence should be written in a .txt file. In the example with DNA, every sequence should have symbols A, C, G and T; with RNA without T. Then you need to specify files path (if its in a local directory, just specify the name) in count_nucleotides().

All the characters in the file need to be type string. You need to go through the file and change every single character to string. This can be done by using:

    ls = [ str(element) for element in ls ]

Counting nucleotides

When every element is string type, we can go through every element and with if statements, that way each element will be automatically assigned to its list:

note: There is a list made for every nucleotide.

    for element in line:

        if (element == 'A'): ls_a_amount.append(element)       # find adenine

        elif (element == 'C'): ls_c_amount.append(element)     # find cytosine

        elif (element == 'G'): ls_g_amount.append(element)     # find guanine

        elif (element == 'T'): ls_t_amount.append(element)     # find thymine

Length of each list will be saved in a dictionary.

The count_nucleotides() returns the amount of every nucleotide which is stored in a dictionary (key is the nucleotide and value length of each list):

    dict_nucleotides = { 'A' : len(ls_s_a) ,'C' : len(ls_s_c), 'G' : len(ls_s_g), 'T' : len(ls_s_t) }

Counting percentage of each nucleotide

The length of lists will be added to one "main" list of data. We need to have the number of all nucleotides and that's why the sum() needs to be used on the main list.

We loop through that same list and divide every element by the sum of main list, and multiply the value by 100 to get the percentage. Add that value to ls_percentage list:

    for element in ls_main:
        
        val = ( element / sum(ls_main) ) * 100

        ls_percentage.append( val )

When that is done, elements from ls_percentage will be added into a dictionary which can be returned by the function.

display_nucleotide_chart()

This function does what it says it does. function takes a dict type argument dict_data which is a dictionary with one key and value.

Key is the protein name, key is the amount of these proteins in a list:

    dict_data[ "nucleotides" ] = ls_all_protein

Pie charts displayed below:

Note

I will be adding more features in the future